Partial merge of mainline develop

166 files changed, 6592 insertions, 2926 deletions

diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index accf09cc2a..15db2f7a16 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -149,26 +149,46 @@ customize an installation in :ref:`sec-specs`.
 ``spack uninstall``
 ~~~~~~~~~~~~~~~~~~~~~
 
-To uninstall a package, type ``spack uninstall <package>``.  This will
-completely remove the directory in which the package was installed.
+To uninstall a package, type ``spack uninstall <package>``.  This will ask the user for
+confirmation, and in case will completely remove the directory in which the package was installed.
 
 .. code-block:: sh
 
    spack uninstall mpich
 
 If there are still installed packages that depend on the package to be
-uninstalled, spack will refuse to uninstall it. You can override this
-behavior with ``spack uninstall -f <package>``, but you risk breaking
-other installed packages. In general, it is safer to remove dependent
-packages *before* removing their dependencies.
+uninstalled, spack will refuse to uninstall it.
 
-A line like ``spack uninstall mpich`` may be ambiguous, if multiple
-``mpich`` configurations are installed.  For example, if both
+To uninstall a package and every package that depends on it, you may give the
+`--dependents` option.
+
+.. code-block:: sh
+
+   spack uninstall --dependents mpich
+
+will display a list of all the packages that depends on `mpich` and, upon confirmation,
+will uninstall them in the right order.
+
+A line like
+
+.. code-block:: sh
+
+   spack uninstall mpich
+
+may be ambiguous, if multiple ``mpich`` configurations are installed.  For example, if both
 ``mpich@3.0.2`` and ``mpich@3.1`` are installed, ``mpich`` could refer
 to either one. Because it cannot determine which one to uninstall,
-Spack will ask you to provide a version number to remove the
-ambiguity.  As an example, ``spack uninstall mpich@3.1`` is
-unambiguous in this scenario.
+Spack will ask you either to provide a version number to remove the
+ambiguity or use the ``--all`` option to uninstall all of the matching packages.
+
+You may force uninstall a package with the `--force` option
+
+.. code-block:: sh
+
+   spack uninstall --force mpich
+
+but you risk breaking other installed packages. In general, it is safer to remove dependent
+packages *before* removing their dependencies or use the `--dependents` option.
 
 
 Seeing installed packages
@@ -352,25 +372,32 @@ how this is done is in :ref:`sec-specs`.
 ``spack compiler add``
 ~~~~~~~~~~~~~~~~~~~~~~~
 
+An alias for ``spack compiler find``.
+
+.. _spack-compiler-find:
+
+``spack compiler find``
+~~~~~~~~~~~~~~~~~~~~~~~
+
 If you do not see a compiler in this list, but you want to use it with
-Spack, you can simply run ``spack compiler add`` with the path to
+Spack, you can simply run ``spack compiler find`` with the path to
 where the compiler is installed.  For example::
 
-    $ spack compiler add /usr/local/tools/ic-13.0.079
+    $ spack compiler find /usr/local/tools/ic-13.0.079
     ==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml
         intel@13.0.079
 
-Or you can run ``spack compiler add`` with no arguments to force
+Or you can run ``spack compiler find`` with no arguments to force
 auto-detection.  This is useful if you do not know where compilers are
 installed, but you know that new compilers have been added to your
 ``PATH``.  For example, using dotkit, you might do this::
 
     $ module load gcc-4.9.0
-    $ spack compiler add
+    $ spack compiler find
     ==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml
         gcc@4.9.0
 
-This loads the environment module for gcc-4.9.0 to get it into the
+This loads the environment module for gcc-4.9.0 to add it to
 ``PATH``, and then it adds the compiler to Spack.
 
 .. _spack-compiler-info:
@@ -761,7 +788,7 @@ versions are now filtered out.
 
 .. _shell-support:
 
-Environment modules
+Integration with module systems
 -------------------------------
 
 .. note::
@@ -771,9 +798,50 @@ Environment modules
    interface and/or generated module names may change in future
    versions.
 
-Spack provides some limited integration with environment module
-systems to make it easier to use the packages it provides.
+Spack provides some integration with
+`Environment Modules <http://modules.sourceforge.net/>`_
+and `Dotkit <https://computing.llnl.gov/?set=jobs&page=dotkit>`_ to make
+it easier to use the packages it installed.
+
+
 
+Installing Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to use Spack's generated environment modules, you must have
+installed the *Environment Modules* package.  On many Linux
+distributions, this can be installed from the vendor's repository:
+
+.. code-block:: sh
+
+    yum install environment-modules # (Fedora/RHEL/CentOS)
+    apt-get install environment-modules # (Ubuntu/Debian)
+
+If your Linux distribution does not have
+Environment Modules, you can get it with Spack:
+
+.. code-block:: sh
+
+    spack install environment-modules
+
+
+In this case to activate it automatically you need to add the following two
+lines to your ``.bashrc`` profile (or similar):
+
+.. code-block:: sh
+
+   MODULES_HOME=`spack location -i environment-modules`
+   source ${MODULES_HOME}/Modules/init/bash
+
+If you use a Unix shell other than ``bash``, modify the commands above
+accordingly and source the appropriate file in
+``${MODULES_HOME}/Modules/init/``.
+
+
+.. TODO : Add a similar section on how to install dotkit ?
+
+Spack and module systems
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 You can enable shell support by sourcing some files in the
 ``/share/spack`` directory.
 
@@ -781,7 +849,7 @@ For ``bash`` or ``ksh``, run:
 
 .. code-block:: sh
 
-   . $SPACK_ROOT/share/spack/setup-env.sh
+   . ${SPACK_ROOT}/share/spack/setup-env.sh
 
 For ``csh`` and ``tcsh`` run:
 
@@ -793,17 +861,19 @@ For ``csh`` and ``tcsh`` run:
 You can put the above code in your ``.bashrc`` or ``.cshrc``, and
 Spack's shell support will be available on the command line.
 
-When you install a package with Spack, it automatically generates an
-environment module that lets you add the package to your environment.
+When you install a package with Spack, it automatically generates a module file
+that lets you add the package to your environment.
 
-Currently, Spack supports the generation of `TCL Modules
+Currently, Spack supports the generation of `Environment Modules
 <http://wiki.tcl.tk/12999>`_ and `Dotkit
 <https://computing.llnl.gov/?set=jobs&page=dotkit>`_.  Generated
 module files for each of these systems can be found in these
 directories:
 
-  * ``$SPACK_ROOT/share/spack/modules``
-  * ``$SPACK_ROOT/share/spack/dotkit``
+.. code-block:: sh
+
+  ${SPACK_ROOT}/share/spack/modules
+  ${SPACK_ROOT}/share/spack/dotkit
 
 The directories are automatically added to your ``MODULEPATH`` and
 ``DK_NODE`` environment variables when you enable Spack's `shell
@@ -859,8 +929,7 @@ of installed packages.
 
 The names here should look familiar, they're the same ones from
 ``spack find``.  You *can* use the names here directly.  For example,
-you could type either of these commands to load the callpath module
-(assuming dotkit and modules are installed):
+you could type either of these commands to load the callpath module:
 
 .. code-block:: sh
 
@@ -875,7 +944,7 @@ easy to type.  Luckily, Spack has its own interface for using modules
 and dotkits.  You can use the same spec syntax you're used to:
 
   =========================  ==========================
-  Modules                    Dotkit
+  Environment Modules        Dotkit
   =========================  ==========================
   ``spack load <spec>``      ``spack use <spec>``
   ``spack unload <spec>``    ``spack unuse <spec>``
@@ -942,15 +1011,216 @@ used ``gcc``.  You could therefore just type:
 
 To identify just the one built with the Intel compiler.
 
+Module files generation and customization
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Environment Modules and Dotkit files are generated when packages are installed,
+and are placed in the following directories under the Spack root:
+
+.. code-block:: sh
+
+  ${SPACK_ROOT}/share/spack/modules
+  ${SPACK_ROOT}/share/spack/dotkit
+
+The content that gets written in each module file can be customized in two ways:
+
+  1. overriding part of the ``spack.Package`` API within a ``package.py``
+  2. writing dedicated configuration files
+
+Override ``Package`` API
+^^^^^^^^^^^^^^^^^^^^^^^^
+There are currently two methods in ``spack.Package`` that may affect the content
+of module files:
+
+.. code-block:: python
+
+  def setup_environment(self, spack_env, run_env):
+      """Set up the compile and runtime environments for a package."""
+      pass
+
+.. code-block:: python
+
+  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+      """Set up the environment of packages that depend on this one"""
+      pass
+
+As briefly stated in the comments, the first method lets you customize the
+module file content for the package you are currently writing, the second
+allows for modifications to your dependees module file. In both cases one
+needs to fill ``run_env`` with the desired list of environment modifications.
+
+Example : ``builtin/packages/python/package.py``
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+The ``python`` package that comes with the ``builtin`` Spack repository
+overrides ``setup_dependent_environment`` in the following way:
+
+.. code-block:: python
 
-Regenerating Module files
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+  def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        # ...
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
 
-Module and dotkit files are generated when packages are installed, and
-are placed in the following directories under the Spack root:
+to insert the appropriate ``PYTHONPATH`` modifications in the module
+files of python packages.
 
-  * ``$SPACK_ROOT/share/spack/modules``
-  * ``$SPACK_ROOT/share/spack/dotkit``
+Configuration files
+^^^^^^^^^^^^^^^^^^^
+
+Another way of modifying the content of module files is writing a
+``modules.yaml`` configuration file. Following usual Spack conventions, this
+file can be placed either at *site* or *user* scope.
+
+The default site configuration reads:
+
+ .. literalinclude:: ../../../etc/spack/modules.yaml
+    :language: yaml
+
+It basically inspects the installation prefixes for the
+existence of a few folders and, if they exist, it prepends a path to a given
+list of environment variables.
+
+For each module system that can be enabled a finer configuration is possible:
+
+.. code-block:: yaml
+
+ modules:
+   tcl:
+     # contains environment modules specific customizations
+   dotkit:
+     # contains dotkit specific customizations
+
+The structure under the ``tcl`` and ``dotkit`` keys is almost equal, and will
+be showcased in the following by some examples.
+
+Select module files by spec constraints
+"""""""""""""""""""""""""""""""""""""""
+Using spec syntax it's possible to have different customizations for different
+groups of module files.
+
+Considering :
+
+.. code-block:: yaml
+
+ modules:
+   tcl:
+     all: # Default addition for every package
+       environment:
+         set:
+           BAR: 'bar'
+     ^openmpi:: # A double ':' overrides previous rules
+       environment:
+         set:
+           BAR: 'baz'
+     zlib:
+       environment:
+         prepend_path:
+           LD_LIBRARY_PATH: 'foo'
+     zlib%gcc@4.8:
+       environment:
+         unset:
+         - FOOBAR
+
+what will happen is that:
+
+ - every module file will set ``BAR=bar``
+ - unless the associated spec satisfies ``^openmpi`` in which case ``BAR=baz``
+ - any spec that satisfies ``zlib`` will additionally prepend ``foo`` to ``LD_LIBRARY_PATH``
+ - any spec that satisfies ``zlib%gcc@4.8`` will additionally unset ``FOOBAR``
+
+.. note::
+  Order does matter
+    The modifications associated with the ``all`` keyword are always evaluated
+    first, no matter where they appear in the configuration file. All the other
+    spec constraints are instead evaluated top to bottom.
+
+Filter modifications out of module files
+""""""""""""""""""""""""""""""""""""""""
+
+Modifications to certain environment variables in module files are generated by
+default. Suppose you would like to avoid having ``CPATH`` and ``LIBRARY_PATH``
+modified by your dotkit modules. Then :
+
+.. code-block:: yaml
+
+  modules:
+    dotkit:
+      all:
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']  # Exclude changes to any of these variables
+
+will generate dotkit module files that will not contain modifications to either
+``CPATH`` or ``LIBRARY_PATH`` and environment module files that instead will
+contain those modifications.
+
+Autoload dependencies
+"""""""""""""""""""""
+
+The following lines in ``modules.yaml``:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      all:
+        autoload: 'direct'
+
+will produce environment module files that will automatically load their direct
+dependencies.
+
+.. note::
+  Allowed values for ``autoload`` statements
+    Allowed values for ``autoload`` statements are either ``none``, ``direct``
+    or ``all``. In ``tcl`` configuration it is possible to use the option
+    ``prerequisites`` that accepts the same values and will add ``prereq``
+    statements instead of automatically loading other modules.
+
+Blacklist or whitelist the generation of specific module files
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Sometimes it is desirable not to generate module files, a common use case being
+not providing the users with software built using the system compiler.
+
+A configuration file like:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      whitelist: ['gcc', 'llvm']  # Whitelist will have precedence over blacklist
+      blacklist: ['%gcc@4.4.7']  # Assuming gcc@4.4.7 is the system compiler
+
+will skip module file generation for anything that satisfies ``%gcc@4.4.7``,
+with the exception of specs that satisfy ``gcc`` or ``llvm``.
+
+Customize the naming scheme and insert conflicts
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+A configuration file like:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
+      all:
+        conflict: ['{name}', 'intel/14.0.1']
+
+will create module files that will conflict with ``intel/14.0.1`` and with the
+base directory of the same module, effectively preventing the possibility to
+load two or more versions of the same software at the same time.
+
+.. note::
+  Tokens available for the naming scheme
+    currently only the tokens shown in the example are available to construct
+    the naming scheme
+
+.. note::
+  The ``conflict`` option is ``tcl`` specific
+
+Regenerating module files
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Sometimes you may need to regenerate the modules files.  For example,
 if newer, fancier module support is added to Spack at some later date,
@@ -960,7 +1230,7 @@ new features.
 .. _spack-module:
 
 ``spack module refresh``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+""""""""""""""""""""""""
 
 Running ``spack module refresh`` will remove the
 ``share/spack/modules`` and ``share/spack/dotkit`` directories, then
@@ -1186,6 +1456,51 @@ several variants:
 
        spack deactivate -a python
 
+Filesystem requirements
+--------------------------
+
+Spack currently needs to be run from a filesystem that supports
+``flock`` locking semantics.  Nearly all local filesystems and recent
+versions of NFS support this, but parallel filesystems may be mounted
+without ``flock`` support enabled.  You can determine how your
+filesystems are mounted with ``mount -p``.  The output for a Lustre
+filesystem might look like this:
+
+.. code-block:: sh
+
+   $ mount -l | grep lscratch
+   pilsner-mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
+   porter-mds1-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
+
+Note the ``flock`` option on both Lustre mounts.  If you do not see
+this or a similar option for your filesystem, you may need ot ask your
+system administrator to enable ``flock``.
+
+This issue typically manifests with the error below:
+
+.. code-block:: sh
+
+   $ ./spack find
+   Traceback (most recent call last):
+   File "./spack", line 176, in <module>
+     main()
+   File "./spack", line 154, in main
+     return_val = command(parser, args)
+   File "./spack/lib/spack/spack/cmd/find.py", line 170, in find
+     specs = set(spack.installed_db.query(**q_args))
+   File "./spack/lib/spack/spack/database.py", line 551, in query
+     with self.read_transaction():
+   File "./spack/lib/spack/spack/database.py", line 598, in __enter__
+     if self._enter() and self._acquire_fn:
+   File "./spack/lib/spack/spack/database.py", line 608, in _enter
+     return self._db.lock.acquire_read(self._timeout)
+   File "./spack/lib/spack/llnl/util/lock.py", line 103, in acquire_read
+     self._lock(fcntl.LOCK_SH, timeout)   # can raise LockError.
+   File "./spack/lib/spack/llnl/util/lock.py", line 64, in _lock
+     fcntl.lockf(self._fd, op | fcntl.LOCK_NB)
+   IOError: [Errno 38] Function not implemented
+
+A nicer error message is TBD in future versions of Spack.
 
 Getting Help
 -----------------------
diff --git a/lib/spack/docs/index.rst b/lib/spack/docs/index.rst
index 79757208c9..d6ce52b747 100644
--- a/lib/spack/docs/index.rst
+++ b/lib/spack/docs/index.rst
@@ -18,7 +18,7 @@ configurations can coexist on the same system.
 Most importantly, Spack is *simple*.  It offers a simple *spec* syntax
 so that users can specify versions and configuration options
 concisely.  Spack is also simple for package authors: package files
-are writtin in pure Python, and specs allow package authors to
+are written in pure Python, and specs allow package authors to
 maintain a single file for many different builds of the same package.
 
 See the :doc:`features` for examples and highlights.
diff --git a/lib/spack/docs/mirrors.rst b/lib/spack/docs/mirrors.rst
index b20fedb55f..dad04d053b 100644
--- a/lib/spack/docs/mirrors.rst
+++ b/lib/spack/docs/mirrors.rst
@@ -38,7 +38,7 @@ contains tarballs for each package, named after each package.
 
 .. note::
 
-   Archives are **not** named exactly they were in the package's fetch
+   Archives are **not** named exactly the way they were in the package's fetch
    URL.  They have the form ``<name>-<version>.<extension>``, where
    ``<name>`` is Spack's name for the package, ``<version>`` is the
    version of the tarball, and ``<extension>`` is whatever format the
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index ef9fd89b62..650e0ee3b2 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -419,7 +419,7 @@ directory to the directory containing the downloaded archive before it
 calls your ``install`` method.  Within ``install``, the path to the
 downloaded archive is available as ``self.stage.archive_file``.
 
-Here is an example snippet for packages distribuetd as self-extracting
+Here is an example snippet for packages distributed as self-extracting
 archives.  The example sets permissions on the downloaded file to make
 it executable, then runs it with some arguments.
 
@@ -703,6 +703,127 @@ Fetching a revision
 Subversion branches are handled as part of the directory structure, so
 you can check out a branch or tag by changing the ``url``.
 
+
+.. _license:
+
+Licensed software
+------------------------------------------
+
+In order to install licensed software, Spack needs to know a few more
+details about a package. The following class attributes should be defined.
+
+``license_required``
+~~~~~~~~~~~~~~~~~~~~~
+
+Boolean. If set to ``True``, this software requires a license. If set to
+``False``, all of the following attributes will be ignored. Defaults to
+``False``.
+
+``license_comment``
+~~~~~~~~~~~~~~~~~~~~~
+
+String. Contains the symbol used by the license manager to denote a comment.
+Defaults to ``#``.
+
+``license_files``
+~~~~~~~~~~~~~~~~~~~~~
+
+List of strings. These are files that the software searches for when
+looking for a license. All file paths must be relative to the installation
+directory. More complex packages like Intel may require multiple
+licenses for individual components. Defaults to the empty list.
+
+``license_vars``
+~~~~~~~~~~~~~~~~~~~~~
+
+List of strings. Environment variables that can be set to tell the software
+where to look for a license if it is not in the usual location. Defaults
+to the empty list.
+
+``license_url``
+~~~~~~~~~~~~~~~~~~~~~
+
+String. A URL pointing to license setup instructions for the software.
+Defaults to the empty string.
+
+For example, let's take a look at the package for the PGI compilers.
+
+.. code-block:: python
+
+    # Licensing
+    license_required = True
+    license_comment  = '#'
+    license_files    = ['license.dat']
+    license_vars     = ['PGROUPD_LICENSE_FILE', 'LM_LICENSE_FILE']
+    license_url      = 'http://www.pgroup.com/doc/pgiinstall.pdf'
+
+As you can see, PGI requires a license. Its license manager, FlexNet, uses
+the ``#`` symbol to denote a comment. It expects the license file to be
+named ``license.dat`` and to be located directly in the installation prefix.
+If you would like the installation file to be located elsewhere, simply set
+``PGROUPD_LICENSE_FILE`` or ``LM_LICENSE_FILE`` after installation. For
+further instructions on installation and licensing, see the URL provided.
+
+Let's walk through a sample PGI installation to see exactly what Spack is
+and isn't capable of. Since PGI does not provide a download URL, it must
+be downloaded manually. It can either be added to a mirror or located in
+the current directory when ``spack install pgi`` is run. See :ref:`mirrors`
+for instructions on setting up a mirror.
+
+After running ``spack install pgi``, the first thing that will happen is
+Spack will create a global license file located at
+``$SPACK_ROOT/etc/spack/licenses/pgi/license.dat``. It will then open up the
+file using the editor set in ``$EDITOR``, or vi if unset. It will look like
+this:
+
+.. code-block::
+
+    # A license is required to use pgi.
+    #
+    # The recommended solution is to store your license key in this global
+    # license file. After installation, the following symlink(s) will be
+    # added to point to this file (relative to the installation prefix):
+    #
+    #   license.dat
+    #
+    # Alternatively, use one of the following environment variable(s):
+    #
+    #   PGROUPD_LICENSE_FILE
+    #   LM_LICENSE_FILE
+    #
+    # If you choose to store your license in a non-standard location, you may
+    # set one of these variable(s) to the full pathname to the license file, or
+    # port@host if you store your license keys on a dedicated license server.
+    # You will likely want to set this variable in a module file so that it
+    # gets loaded every time someone tries to use pgi.
+    #
+    # For further information on how to acquire a license, please refer to:
+    #
+    #   http://www.pgroup.com/doc/pgiinstall.pdf
+    #
+    # You may enter your license below.
+
+You can add your license directly to this file, or tell FlexNet to use a
+license stored on a separate license server. Here is an example that
+points to a license server called licman1:
+
+.. code-block::
+
+    SERVER licman1.mcs.anl.gov 00163eb7fba5 27200
+    USE_SERVER
+
+If your package requires the license to install, you can reference the
+location of this global license using ``self.global_license_file``.
+After installation, symlinks for all of the files given in
+``license_files`` will be created, pointing to this global license.
+If you install a different version or variant of the package, Spack
+will automatically detect and reuse the already existing global license.
+
+If the software you are trying to package doesn't rely on license files,
+Spack will print a warning message, letting the user know that they
+need to set an environment variable or pointing them to installation
+documentation.
+
 .. _patching:
 
 Patches
@@ -1556,14 +1677,14 @@ you ask for a particular spec.
 ``Concretization Policies``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-A user may have certain perferrences for how packages should
+A user may have certain preferences for how packages should
 be concretized on their system.  For example, one user may prefer packages
 built with OpenMPI and the Intel compiler.  Another user may prefer
-packages be built with MVAPICH and GCC.  
+packages be built with MVAPICH and GCC.
 
-Spack can be configurated to prefer certain compilers, package
+Spack can be configured to prefer certain compilers, package
 versions, depends_on, and variants during concretization.
-The preferred configuration can be controlled via the 
+The preferred configuration can be controlled via the
 ``~/.spack/packages.yaml`` file for user configuations, or the
 ``etc/spack/packages.yaml`` site configuration.
 
@@ -1582,32 +1703,32 @@ Here's an example packages.yaml file that sets preferred packages:
         compiler: [gcc@4.4.7, gcc@4.6:, intel, clang, pgi]
         providers:
           mpi: [mvapich, mpich, openmpi]
-          
+
 
 At a high level, this example is specifying how packages should be
-concretized.  The dyninst package should prefer using gcc 4.9 and 
+concretized.  The dyninst package should prefer using gcc 4.9 and
 be built with debug options.  The gperftools package should prefer version
 2.2 over 2.4.  Every package on the system should prefer mvapich for
-its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by perfering gcc 4.9).  
-These options are used to fill in implicit defaults.  Any of them can be overwritten 
+its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9).
+These options are used to fill in implicit defaults.  Any of them can be overwritten
 on the command line if explicitly requested.
 
-Each packages.yaml file begin with the string ``packages:`` and 
+Each packages.yaml file begins with the string ``packages:`` and
 package names are specified on the next level. The special string ``all``
-applies settings to each package. Underneath each package name is 
-one or more components: ``compiler``, ``variants``, ``version``, 
-or ``providers``.  Each component has an ordered list of spec 
-``constraints``, with earlier entries in the list being prefered over
+applies settings to each package. Underneath each package name is
+one or more components: ``compiler``, ``variants``, ``version``,
+or ``providers``.  Each component has an ordered list of spec
+``constraints``, with earlier entries in the list being preferred over
 later entries.
 
-Sometimes a package installation may have constraints that forbid 
+Sometimes a package installation may have constraints that forbid
 the first concretization rule, in which case Spack will use the first
 legal concretization rule.  Going back to the example, if a user
-requests gperftools 2.3 or later, then Spack will install version 2.4 
+requests gperftools 2.3 or later, then Spack will install version 2.4
 as the 2.4 version of gperftools is preferred over 2.3.
 
-An explicit concretization rule in the preferred section will always 
-take preference over unlisted concretizations.  In the above example, 
+An explicit concretization rule in the preferred section will always
+take preference over unlisted concretizations.  In the above example,
 xlc isn't listed in the compiler list.  Every listed compiler from
 gcc to pgi will thus be preferred over the xlc compiler.
 
@@ -1803,15 +1924,15 @@ Compile-time library search paths
   * ``-L$dep_prefix/lib``
   * ``-L$dep_prefix/lib64``
 Runtime library search paths (RPATHs)
-  * ``-Wl,-rpath,$dep_prefix/lib``
-  * ``-Wl,-rpath,$dep_prefix/lib64``
+  * ``$rpath_flag$dep_prefix/lib``
+  * ``$rpath_flag$dep_prefix/lib64``
 Include search paths
   * ``-I$dep_prefix/include``
 
 An example of this would be the ``libdwarf`` build, which has one
 dependency: ``libelf``.  Every call to ``cc`` in the ``libdwarf``
 build will have ``-I$LIBELF_PREFIX/include``,
-``-L$LIBELF_PREFIX/lib``, and ``-Wl,-rpath,$LIBELF_PREFIX/lib``
+``-L$LIBELF_PREFIX/lib``, and ``$rpath_flag$LIBELF_PREFIX/lib``
 inserted on the command line.  This is done transparently to the
 project's build system, which will just think it's using a system
 where ``libelf`` is readily available.  Because of this, you **do
@@ -1831,6 +1952,48 @@ successfully find ``libdwarf.h`` and ``libdwarf.so``, without the
 packager having to provide ``--with-libdwarf=/path/to/libdwarf`` on
 the command line.
 
+.. note::
+
+    For most compilers, ``$rpath_flag`` is ``-Wl,-rpath,``. However, NAG
+    passes its flags to GCC instead of passing them directly to the linker.
+    Therefore, its ``$rpath_flag`` is doubly wrapped: ``-Wl,-Wl,,-rpath,``.
+    ``$rpath_flag`` can be overriden on a compiler specific basis in
+    ``lib/spack/spack/compilers/$compiler.py``.
+
+Compiler flags
+~~~~~~~~~~~~~~
+In rare circumstances such as compiling and running small unit tests, a package
+developer may need to know what are the appropriate compiler flags to enable
+features like ``OpenMP``, ``c++11``, ``c++14`` and alike. To that end the
+compiler classes in ``spack`` implement the following _properties_ :
+``openmp_flag``, ``cxx11_flag``, ``cxx14_flag``, which can be accessed in a
+package by ``self.compiler.cxx11_flag`` and alike. Note that the implementation
+is such that if a given compiler version does not support this feature, an
+error will be produced. Therefore package developers can also use these properties
+to assert that a compiler supports the requested feature. This is handy when a
+package supports additional variants like
+
+.. code-block:: python
+
+   variant('openmp', default=True, description="Enable OpenMP support.")
+
+Message Parsing Interface (MPI)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+It is common for high performance computing software/packages to use ``MPI``.
+As a result of conretization, a given package can be built using different
+implementations of MPI such as ``Openmpi``, ``MPICH`` or ``IntelMPI``.
+In some scenarios to configure a package one have to provide it with appropriate MPI
+compiler wrappers such as ``mpicc``, ``mpic++``.
+However different implementations of ``MPI`` may have different names for those
+wrappers.  In order to make package's ``install()`` method indifferent to the
+choice ``MPI`` implementation, each package which implements ``MPI`` sets up
+``self.spec.mpicc``, ``self.spec.mpicxx``, ``self.spec.mpifc`` and ``self.spec.mpif77``
+to point to ``C``, ``C++``, ``Fortran 90`` and ``Fortran 77`` ``MPI`` wrappers.
+Package developers are advised to use these variables, for example ``self.spec['mpi'].mpicc``
+instead of hard-coding ``join_path(self.spec['mpi'].prefix.bin, 'mpicc')`` for
+the reasons outlined above.
+
+
 Forking ``install()``
 ~~~~~~~~~~~~~~~~~~~~~
 
@@ -1844,6 +2007,20 @@ dedicated process.
 
 .. _prefix-objects:
 
+
+Failing the build
+----------------------
+
+Sometimes you don't want a package to successfully install unless some
+condition is true.  You can explicitly cause the build to fail from
+``install()`` by raising an ``InstallError``, for example:
+
+.. code-block:: python
+
+   if spec.architecture.startswith('darwin'):
+       raise InstallError('This package does not build on Mac OS X!')
+
+
 Prefix objects
 ----------------------
 
@@ -2160,6 +2337,62 @@ package, this allows us to avoid race conditions in the library's
 build system.
 
 
+.. _sanity-checks:
+
+Sanity checking an intallation
+--------------------------------
+
+By default, Spack assumes that a build has failed if nothing is
+written to the install prefix, and that it has succeeded if anything
+(a file, a directory, etc.)  is written to the install prefix after
+``install()`` completes.
+
+Consider a simple autotools build like this:
+
+.. code-block:: python
+
+   def install(self, spec, prefix):
+       configure("--prefix=" + prefix)
+       make()
+       make("install")
+
+If you are using using standard autotools or CMake, ``configure`` and
+``make`` will not write anything to the install prefix.  Only ``make
+install`` writes the files, and only once the build is already
+complete.  Not all builds are like this.  Many builds of scientific
+software modify the install prefix *before* ``make install``. Builds
+like this can falsely report that they were successfully installed if
+an error occurs before the install is complete but after files have
+been written to the ``prefix``.
+
+
+``sanity_check_is_file`` and ``sanity_check_is_dir``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You can optionally specify *sanity checks* to deal with this problem.
+Add properties like this to your package:
+
+.. code-block:: python
+
+   class MyPackage(Package):
+       ...
+
+       sanity_check_is_file = ['include/libelf.h']
+       sanity_check_is_dir  = [lib]
+
+       def install(self, spec, prefix):
+           configure("--prefix=" + prefix)
+           make()
+           make("install")
+
+Now, after ``install()`` runs, Spack will check whether
+``$prefix/include/libelf.h`` exists and is a file, and whether
+``$prefix/lib`` exists and is a directory.  If the checks fail, then
+the build will fail and the install prefix will be removed.  If they
+succeed, Spack considers the build succeeful and keeps the prefix in
+place.
+
+
 .. _file-manipulation:
 
 File manipulation functions
diff --git a/lib/spack/docs/site_configuration.rst b/lib/spack/docs/site_configuration.rst
index 76fe8fdd7d..3abfa21a9d 100644
--- a/lib/spack/docs/site_configuration.rst
+++ b/lib/spack/docs/site_configuration.rst
@@ -56,7 +56,7 @@ directory is.
 
 External Packages
 ~~~~~~~~~~~~~~~~~~~~~
-Spack can be configured to use externally-installed 
+Spack can be configured to use externally-installed
 packages rather than building its own packages. This may be desirable
 if machines ship with system packages, such as a customized MPI
 that should be used instead of Spack building its own MPI.
@@ -76,21 +76,20 @@ directory. Here's an example of an external configuration:
 
 This example lists three installations of OpenMPI, one built with gcc,
 one built with gcc and debug information, and another built with Intel.
-If Spack is asked to build a package that uses one of these MPIs as a 
+If Spack is asked to build a package that uses one of these MPIs as a
 dependency, it will use the the pre-installed OpenMPI in
-the given directory.  This example also specifies that Spack should never
-build its own OpenMPI via the ``nobuild: True`` option.
+the given directory.  
 
 Each ``packages.yaml`` begins with a ``packages:`` token, followed
 by a list of package names.  To specify externals, add a ``paths``
 token under the package name, which lists externals in a
 ``spec : /path`` format.  Each spec should be as
-well-defined as reasonably possible.  If a 
-package lacks a spec component, such as missing a compiler or 
-package version, then Spack will guess the missing component based 
+well-defined as reasonably possible.  If a
+package lacks a spec component, such as missing a compiler or
+package version, then Spack will guess the missing component based
 on its most-favored packages, and it may guess incorrectly.
 
-Each package version and compilers listed in an external should 
+Each package version and compilers listed in an external should
 have entries in Spack's packages and compiler configuration, even
 though the package and compiler may not every be built.
 
@@ -112,17 +111,17 @@ be:
         openmpi@1.4.3%gcc@4.4.7=chaos_5_x86_64_ib: /opt/openmpi-1.4.3
         openmpi@1.4.3%gcc@4.4.7=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug
         openmpi@1.6.5%intel@10.1=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel                
-    nobuild: True
+      buildable: False
 
-The addition of the ``nobuild`` flag tells Spack that it should never build
+The addition of the ``buildable`` flag tells Spack that it should never build
 its own version of OpenMPI, and it will instead always rely on a pre-built
-OpenMPI.  Similar to ``paths``, ``nobuild`` is specified as a property under
+OpenMPI.  Similar to ``paths``, ``buildable`` is specified as a property under
 a package name.
 
-The ``nobuild`` does not need to be paired with external packages.  
+The ``buildable`` does not need to be paired with external packages.  
 It could also be used alone to forbid packages that may be 
 buggy or otherwise undesirable.
-  
+
 
 Profiling
 ~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 91916c4532..9758b74f37 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -1,27 +1,27 @@
 #!/bin/bash
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 #
 # Spack compiler wrapper script.
@@ -38,19 +38,27 @@
 #      -Wl,-rpath   arguments for dependency /lib directories.
 #
 
-# This is the list of environment variables that need to be set before
-# the script runs.  They are set by routines in spack.build_environment
+# This is an array of environment variables that need to be set before
+# the script runs. They are set by routines in spack.build_environment
 # as part of spack.package.Package.do_install().
-parameters="
-SPACK_PREFIX
-SPACK_ENV_PATH
-SPACK_DEBUG_LOG_DIR
-SPACK_COMPILER_SPEC
-SPACK_SHORT_SPEC"
+parameters=(
+    SPACK_PREFIX
+    SPACK_ENV_PATH
+    SPACK_DEBUG_LOG_DIR
+    SPACK_COMPILER_SPEC
+    SPACK_CC_RPATH_ARG
+    SPACK_CXX_RPATH_ARG
+    SPACK_F77_RPATH_ARG
+    SPACK_FC_RPATH_ARG
+    SPACK_SHORT_SPEC
+)
 
 # The compiler input variables are checked for sanity later:
 #   SPACK_CC, SPACK_CXX, SPACK_F77, SPACK_FC
-# Debug flag is optional; set to true for debug logging:
+# The default compiler flags are passed from these variables:
+#   SPACK_CFLAGS, SPACK_CXXFLAGS, SPACK_FCFLAGS, SPACK_FFLAGS,
+#   SPACK_LDFLAGS, SPACK_LDLIBS
+# Debug env var is optional; set to true for debug logging:
 #   SPACK_DEBUG
 # Test command is used to unit test the compiler script.
 #   SPACK_TEST_COMMAND
@@ -64,13 +72,12 @@ function die {
     exit 1
 }
 
-for param in $parameters; do
-    if [ -z "${!param}" ]; then
-        die "Spack compiler must be run from spack!  Input $param was missing!"
+for param in ${parameters[@]}; do
+    if [[ -z ${!param} ]]; then
+        die "Spack compiler must be run from Spack! Input '$param' is missing."
     fi
 done
 
-#
 # Figure out the type of compiler, the language, and the mode so that
 # the compiler script knows what to do.
 #
@@ -78,32 +85,42 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    vcheck  version check
+#    cpp     preprocess
 #    cc      compile
+#    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    cpp     preprocessor
-#    vcheck  version check
-#
+
 command=$(basename "$0")
+comp="CC"
 case "$command" in
+    cpp)
+        mode=cpp
+        ;;
     cc|c89|c99|gcc|clang|icc|pgcc|xlc)
         command="$SPACK_CC"
         language="C"
+        comp="CC"
+        lang_flags=C
         ;;
     c++|CC|g++|clang++|icpc|pgc++|xlc++)
         command="$SPACK_CXX"
         language="C++"
+        comp="CXX"
+        lang_flags=CXX
         ;;
     f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor)
         command="$SPACK_FC"
         language="Fortran 90"
+        comp="FC"
+        lang_flags=F
         ;;
     f77|gfortran|ifort|pgfortran|xlf|nagfor)
         command="$SPACK_F77"
         language="Fortran 77"
-        ;;
-    cpp)
-        mode=cpp
+        comp="F77"
+        lang_flags=F
         ;;
     ld)
         mode=ld
@@ -113,226 +130,155 @@ case "$command" in
         ;;
 esac
 
-# If any of the arguments below is present then the mode is vcheck. In vcheck mode nothing is added in terms of extra search paths or libraries
-if [ -z "$mode" ]; then
+# If any of the arguments below are present, then the mode is vcheck.
+# In vcheck mode, nothing is added in terms of extra search paths or
+# libraries.
+if [[ -z $mode ]]; then
     for arg in "$@"; do
-        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
+        if [[ $arg == -v || $arg == -V || $arg == --version || $arg == -dumpversion ]]; then
             mode=vcheck
             break
-    fi
+        fi
     done
 fi
 
 # Finish setting up the mode.
-
-if [ -z "$mode" ]; then
+if [[ -z $mode ]]; then
     mode=ccld
     for arg in "$@"; do
-        if [ "$arg" = -E ]; then
+        if [[ $arg == -E ]]; then
             mode=cpp
             break
-        elif [ "$arg" = -c ]; then
+        elif [[ $arg == -S ]]; then
+            mode=as
+            break
+        elif [[ $arg == -c ]]; then
             mode=cc
             break
         fi
     done
 fi
 
+# Set up rpath variable according to language.
+eval rpath=\$SPACK_${comp}_RPATH_ARG
+
 # Dump the version and exit if we're in testing mode.
-if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
+if [[ $SPACK_TEST_COMMAND == dump-mode ]]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
+if [[ $mode == vcheck ]]; then
+    exec ${command} "$@"
+fi
+
+# Darwin's linker has a -r argument that merges object files together.
+# It doesn't work with -rpath.
+# This variable controls whether they are added.
+add_rpaths=true
+if [[ $mode == ld && "$SPACK_SHORT_SPEC" =~ "darwin" ]]; then
+    for arg in "$@"; do
+        if [[ $arg == -r ]]; then
+            add_rpaths=false
+            break
+        fi
+    done
+fi
+
 # Save original command for debug logging
 input_command="$@"
+args=("$@")
 
-#
-# Filter '.' and Spack environment directories out of PATH so that
-# this script doesn't just call itself
-#
-IFS=':' read -ra env_path <<< "$PATH"
-IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
-spack_env_dirs+=(".")
-PATH=""
-for dir in "${env_path[@]}"; do
-    remove=""
-    for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
-    done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
-    fi
-done
-export PATH
+# Prepend cppflags, cflags, cxxflags, fcflags, fflags, and ldflags
 
-if [ "$mode" == vcheck ] ; then
-    exec ${command} "$@"
-fi
+# Add ldflags
+case "$mode" in
+    ld|ccld)
+        args=(${SPACK_LDFLAGS[@]} "${args[@]}") ;;
+esac
 
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
+# Add compiler flags.
+case "$mode" in
+    cc|ccld)
+    # Add c, cxx, fc, and f flags
+        case $lang_flags in
+            C)
+                args=(${SPACK_CFLAGS[@]} "${args[@]}") ;;
+            CXX)
+                args=(${SPACK_CXXFLAGS[@]} "${args[@]}") ;;
+        esac
+        ;;
+esac
 
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-            if [[ $arg == -rpath=* ]]; then
-                arg="${arg#-rpath=}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath,* ]]; then
-                arg="${arg#-rpath,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != '-Wl,'* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
-                fi
-                arg="${arg#-Wl,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker)
-            shift; arg="$1";
-            if [[ $arg = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ $arg = -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != -Xlinker ]]; then
-                    die "-Xlinker -rpath was not followed by -Xlinker <arg>"
-                fi
-                shift; arg="$1"
-                rpaths+=("$arg")
-            else
-                other_args+=("-Xlinker")
-                other_args+=("$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
+# Add cppflags
+case "$mode" in
+    cpp|as|cc|ccld)
+        args=(${SPACK_CPPFLAGS[@]} "${args[@]}") ;;
+esac
 
-# Dump parsed values for unit testing if asked for
-if [ -n "$SPACK_TEST_COMMAND" ]; then
-    IFS=$'\n'
-    case "$SPACK_TEST_COMMAND" in
-        dump-includes)   echo "${includes[*]}";;
-        dump-libraries)  echo "${libraries[*]}";;
-        dump-libs)       echo "${libs[*]}";;
-        dump-rpaths)     echo "${rpaths[*]}";;
-        dump-other-args) echo "${other_args[*]}";;
-        dump-all)
-            echo "INCLUDES:"
-            echo "${includes[*]}"
-            echo
-            echo "LIBRARIES:"
-            echo "${libraries[*]}"
-            echo
-            echo "LIBS:"
-            echo "${libs[*]}"
-            echo
-            echo "RPATHS:"
-            echo "${rpaths[*]}"
-            echo
-            echo "ARGS:"
-            echo "${other_args[*]}"
-            ;;
-        *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
-    esac
-    exit
-fi
+case "$mode" in cc|ccld)
+        # Add fortran flags
+        case $lang_flags in
+            F)
+                args=(${SPACK_FFLAGS[@]} "${args[@]}") ;;
+        esac
+        ;;
+esac
 
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
-        includes+=("$dep/include")
+    # Prepend include directories
+    if [[ -d $dep/include ]]; then
+        if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
+            args=("-I$dep/include" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib" ]; then
-        libraries+=("$dep/lib")
-        rpaths+=("$dep/lib")
+    # Prepend lib and RPATH directories
+    if [[ -d $dep/lib ]]; then
+        if [[ $mode == ccld ]]; then
+            $add_rpaths && args=("$rpath$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
+        elif [[ $mode == ld ]]; then
+            $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
-        libraries+=("$dep/lib64")
-        rpaths+=("$dep/lib64")
+    # Prepend lib64 and RPATH directories
+    if [[ -d $dep/lib64 ]]; then
+        if [[ $mode == ccld ]]; then
+            $add_rpaths && args=("$rpath$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
+        elif [[ $mode == ld ]]; then
+            $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
+        fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
-for dir in "${libraries[@]}"; do
-    [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
-done
-rpaths+=("$SPACK_PREFIX/lib")
-rpaths+=("$SPACK_PREFIX/lib64")
-
-# Put the arguments together
-args=()
-for dir in "${includes[@]}";  do args+=("-I$dir"); done
-args+=("${other_args[@]}")
-for dir in "${libraries[@]}"; do args+=("-L$dir"); done
-for lib in "${libs[@]}";      do args+=("-l$lib"); done
-
-if [ "$mode" = ccld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-Wl,-rpath")
-        args+=("-Wl,$dir");
-    done
-elif [ "$mode" = ld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-rpath")
-        args+=("$dir");
-    done
+if [[ $mode == ccld ]]; then
+    $add_rpaths && args=("$rpath$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("$rpath$SPACK_PREFIX/lib"   "${args[@]}")
+elif [[ $mode == ld ]]; then
+    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib"   "${args[@]}")
 fi
 
+# Add SPACK_LDLIBS to args
+case "$mode" in
+    ld|ccld)
+        args=("${args[@]}" ${SPACK_LDLIBS[@]}) ;;
+esac
+
 #
 # Unset pesky environment variables that could affect build sanity.
 #
@@ -340,17 +286,46 @@ unset LD_LIBRARY_PATH
 unset LD_RUN_PATH
 unset DYLD_LIBRARY_PATH
 
-full_command=("$command")
-full_command+=("${args[@]}")
+#
+# Filter '.' and Spack environment directories out of PATH so that
+# this script doesn't just call itself
+#
+IFS=':' read -ra env_path <<< "$PATH"
+IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
+spack_env_dirs+=("" ".")
+PATH=""
+for dir in "${env_path[@]}"; do
+    addpath=true
+    for env_dir in "${spack_env_dirs[@]}"; do
+        if [[ $dir == $env_dir ]]; then
+            addpath=false
+            break
+        fi
+    done
+    if $addpath; then
+        PATH="${PATH:+$PATH:}$dir"
+    fi
+done
+export PATH
+
+full_command=("$command" "${args[@]}")
+
+# In test command mode, write out full command for Spack tests.
+if [[ $SPACK_TEST_COMMAND == dump-args ]]; then
+    echo "${full_command[@]}"
+    exit
+elif [[ -n $SPACK_TEST_COMMAND ]]; then
+    die "ERROR: Unknown test command"
+fi
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [ "$SPACK_DEBUG" = "TRUE" ]; then
+if [[ $SPACK_DEBUG == TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
-    echo "$mode       ${full_command[@]}" >> $output_log
+    echo "[$mode] $command $input_command" >> $input_log
+    echo "[$mode] ${full_command[@]}" >> $output_log
 fi
 
 exec "${full_command[@]}"
diff --git a/lib/spack/external/nose/LICENSE b/lib/spack/external/nose/LICENSE
index 8add30ad59..9f6e791624 100644
--- a/lib/spack/external/nose/LICENSE
+++ b/lib/spack/external/nose/LICENSE
@@ -55,7 +55,7 @@ modified by someone else and passed on, the recipients should know
 that what they have is not the original version, so that the original
 author's reputation will not be affected by problems that might be
 introduced by others.
-
+
   Finally, software patents pose a constant threat to the existence of
 any free program.  We wish to make sure that a company cannot
 effectively restrict the users of a free program by obtaining a
@@ -111,7 +111,7 @@ modification follow.  Pay close attention to the difference between a
 "work based on the library" and a "work that uses the library".  The
 former contains code derived from the library, whereas the latter must
 be combined with the library in order to run.
-
+
 		  GNU LESSER GENERAL PUBLIC LICENSE
    TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
 
@@ -146,7 +146,7 @@ such a program is covered only if its contents constitute a work based
 on the Library (independent of the use of the Library in a tool for
 writing it).  Whether that is true depends on what the Library does
 and what the program that uses the Library does.
-  
+
   1. You may copy and distribute verbatim copies of the Library's
 complete source code as you receive it, in any medium, provided that
 you conspicuously and appropriately publish on each copy an
@@ -158,7 +158,7 @@ Library.
   You may charge a fee for the physical act of transferring a copy,
 and you may at your option offer warranty protection in exchange for a
 fee.
-
+
   2. You may modify your copy or copies of the Library or any portion
 of it, thus forming a work based on the Library, and copy and
 distribute such modifications or work under the terms of Section 1
@@ -216,7 +216,7 @@ instead of to this License.  (If a newer version than version 2 of the
 ordinary GNU General Public License has appeared, then you can specify
 that version instead if you wish.)  Do not make any other change in
 these notices.
-
+
   Once this change is made in a given copy, it is irreversible for
 that copy, so the ordinary GNU General Public License applies to all
 subsequent copies and derivative works made from that copy.
@@ -267,7 +267,7 @@ Library will still fall under Section 6.)
 distribute the object code for the work under the terms of Section 6.
 Any executables containing that work also fall under Section 6,
 whether or not they are linked directly with the Library itself.
-
+
   6. As an exception to the Sections above, you may also combine or
 link a "work that uses the Library" with the Library to produce a
 work containing portions of the Library, and distribute that work
@@ -329,7 +329,7 @@ restrictions of other proprietary libraries that do not normally
 accompany the operating system.  Such a contradiction means you cannot
 use both them and the Library together in an executable that you
 distribute.
-
+
   7. You may place library facilities that are a work based on the
 Library side-by-side in a single library together with other library
 facilities not covered by this License, and distribute such a combined
@@ -370,7 +370,7 @@ subject to these terms and conditions.  You may not impose any further
 restrictions on the recipients' exercise of the rights granted herein.
 You are not responsible for enforcing compliance by third parties with
 this License.
-
+
   11. If, as a consequence of a court judgment or allegation of patent
 infringement or for any other reason (not limited to patent issues),
 conditions are imposed on you (whether by court order, agreement or
@@ -422,7 +422,7 @@ conditions either of that version or of any later version published by
 the Free Software Foundation.  If the Library does not specify a
 license version number, you may choose any version ever published by
 the Free Software Foundation.
-
+
   14. If you wish to incorporate parts of the Library into other free
 programs whose distribution conditions are incompatible with these,
 write to the author to ask for permission.  For software which is
@@ -456,7 +456,7 @@ SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGES.
 
 		     END OF TERMS AND CONDITIONS
-
+
            How to Apply These Terms to Your New Libraries
 
   If you develop a new library, and you want it to be of the greatest
@@ -500,5 +500,3 @@ necessary.  Here is a sample; alter the names:
   Ty Coon, President of Vice
 
 That's all there is to it!
-
-
diff --git a/lib/spack/llnl/__init__.py b/lib/spack/llnl/__init__.py
index e69de29bb2..ed1ec23bca 100644
--- a/lib/spack/llnl/__init__.py
+++ b/lib/spack/llnl/__init__.py
@@ -0,0 +1,24 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
diff --git a/lib/spack/llnl/util/__init__.py b/lib/spack/llnl/util/__init__.py
index e69de29bb2..ed1ec23bca 100644
--- a/lib/spack/llnl/util/__init__.py
+++ b/lib/spack/llnl/util/__init__.py
@@ -0,0 +1,24 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index c4665c284c..6661a80f27 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -1,35 +1,37 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 __all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree',
            'expand_user', 'working_dir', 'touch', 'touchp', 'mkdirp',
            'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree']
+           'remove_dead_links', 'remove_linked_tree', 'find_library_path',
+           'fix_darwin_install_name']
 
 import os
+import glob
 import sys
 import re
 import shutil
@@ -38,6 +40,7 @@ import errno
 import getpass
 from contextlib import contextmanager, closing
 from tempfile import NamedTemporaryFile
+import subprocess
 
 import llnl.util.tty as tty
 from spack.util.compression import ALLOWED_ARCHIVE_TYPES
@@ -392,3 +395,44 @@ def remove_linked_tree(path):
             os.unlink(path)
         else:
             shutil.rmtree(path, True)
+
+
+def fix_darwin_install_name(path):
+    """
+    Fix install name of dynamic libraries on Darwin to have full path.
+    There are two parts of this task:
+    (i) use install_name('-id',...) to change install name of a single lib;
+    (ii) use install_name('-change',...) to change the cross linking between libs.
+    The function assumes that all libraries are in one folder and currently won't
+    follow subfolders.
+
+    Args:
+        path: directory in which .dylib files are alocated
+
+    """
+    libs = glob.glob(join_path(path,"*.dylib"))
+    for lib in libs:
+        # fix install name first:
+        subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0]
+        long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n')
+        deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
+        # fix all dependencies:
+        for dep in deps:
+            for loc in libs:
+                if dep == os.path.basename(loc):
+                    subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0]
+                    break
+
+
+def find_library_path(libname, *paths):
+    """Searches for a file called <libname> in each path.
+
+    Return:
+      directory where the library was found, if found.  None otherwise.
+
+    """
+    for path in paths:
+        library = join_path(path, libname)
+        if os.path.exists(library):
+            return path
+    return None
diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index 1c4d1ed623..63eb08d803 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re
@@ -117,7 +117,8 @@ def caller_locals():
        scope.  Yes, this is some black magic, and yes it's useful
        for implementing things like depends_on and provides.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         return stack[2][0].f_locals
     finally:
@@ -128,7 +129,8 @@ def get_calling_module_name():
     """Make sure that the caller is a class definition, and return the
        enclosing module's name.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         # Make sure locals contain __module__
         caller_locals = stack[2][0].f_locals
@@ -235,11 +237,11 @@ def key_ordering(cls):
     if not has_method(cls, '_cmp_key'):
         raise TypeError("'%s' doesn't define _cmp_key()." % cls.__name__)
 
-    setter('__eq__', lambda s,o: o is not None and s._cmp_key() == o._cmp_key())
+    setter('__eq__', lambda s,o: (s is o) or (o is not None and s._cmp_key() == o._cmp_key()))
     setter('__lt__', lambda s,o: o is not None and s._cmp_key() <  o._cmp_key())
     setter('__le__', lambda s,o: o is not None and s._cmp_key() <= o._cmp_key())
 
-    setter('__ne__', lambda s,o: o is None or s._cmp_key() != o._cmp_key())
+    setter('__ne__', lambda s,o: (s is not o) and (o is None or s._cmp_key() != o._cmp_key()))
     setter('__gt__', lambda s,o: o is None or s._cmp_key() >  o._cmp_key())
     setter('__ge__', lambda s,o: o is None or s._cmp_key() >= o._cmp_key())
 
diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py
index 6ae8aff75c..b6d8796084 100644
--- a/lib/spack/llnl/util/link_tree.py
+++ b/lib/spack/llnl/util/link_tree.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """LinkTree class for setting up trees of symbolic links."""
 __all__ = ['LinkTree']
diff --git a/lib/spack/llnl/util/lock.py b/lib/spack/llnl/util/lock.py
index a7a9bf6b19..479a1b0167 100644
--- a/lib/spack/llnl/util/lock.py
+++ b/lib/spack/llnl/util/lock.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import fcntl
diff --git a/lib/spack/llnl/util/tty/__init__.py b/lib/spack/llnl/util/tty/__init__.py
index 3ecd3a4ac2..c638b113fd 100644
--- a/lib/spack/llnl/util/tty/__init__.py
+++ b/lib/spack/llnl/util/tty/__init__.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import os
diff --git a/lib/spack/llnl/util/tty/colify.py b/lib/spack/llnl/util/tty/colify.py
index 47c3cc4f8f..429ba45882 100644
--- a/lib/spack/llnl/util/tty/colify.py
+++ b/lib/spack/llnl/util/tty/colify.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 Routines for printing columnar output.  See colify() for more information.
diff --git a/lib/spack/llnl/util/tty/color.py b/lib/spack/llnl/util/tty/color.py
index 167a99d3c2..0abcb09b97 100644
--- a/lib/spack/llnl/util/tty/color.py
+++ b/lib/spack/llnl/util/tty/color.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This file implements an expression syntax, similar to printf, for adding
diff --git a/lib/spack/llnl/util/tty/log.py b/lib/spack/llnl/util/tty/log.py
index 22f1087e53..ca82da7b17 100644
--- a/lib/spack/llnl/util/tty/log.py
+++ b/lib/spack/llnl/util/tty/log.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Utility classes for logging the output of blocks of code.
 """
diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index f556b83924..fc6cb06577 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys
@@ -107,7 +107,7 @@ concretizer = DefaultConcretizer()
 
 # Version information
 from spack.version import Version
-spack_version = Version("0.8.15")
+spack_version = Version("0.9")
 
 #
 # Executables used by Spack
@@ -138,9 +138,7 @@ for path in _tmp_candidates:
     # don't add a second username if it's already unique by user.
     if not _tmp_user in path:
         tmp_dirs.append(join_path(path, '%u', 'spack-stage'))
-
-for path in _tmp_candidates:
-    if not path in tmp_dirs:
+    else:
         tmp_dirs.append(join_path(path, 'spack-stage'))
 
 # Whether spack should allow installation of unsafe versions of
@@ -190,3 +188,10 @@ __all__ += spack.directives.__all__
 import spack.util.executable
 from spack.util.executable import *
 __all__ += spack.util.executable.__all__
+
+from spack.package import \
+    install_dependency_symlinks, flatten_dependencies, DependencyConflictError, \
+    InstallError, ExternalPackageError
+__all__ += [
+    'install_dependency_symlinks', 'flatten_dependencies', 'DependencyConflictError',
+    'InstallError', 'ExternalPackageError']
diff --git a/lib/spack/spack/abi.py b/lib/spack/spack/abi.py
index d872952040..38cff62af4 100644
--- a/lib/spack/spack/abi.py
+++ b/lib/spack/spack/abi.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://scalability-llnl.github.io/spack
+# For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 import os
diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py
index 301495f728..d7f908cfb1 100644
--- a/lib/spack/spack/architecture.py
+++ b/lib/spack/spack/architecture.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 from collections import namedtuple
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 8016bc4151..4974cc1e76 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -1,9 +1,33 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 """
 This module contains all routines related to setting up the package
 build environment.  All of this is set up by package.py just before
 install() is called.
 
-There are two parts to the bulid environment:
+There are two parts to the build environment:
 
 1. Python build environment (i.e. install() method)
 
@@ -13,7 +37,7 @@ There are two parts to the bulid environment:
    the package's module scope.  Ths allows package writers to call
    them all directly in Package.install() without writing 'self.'
    everywhere.  No, this isn't Pythonic.  Yes, it makes the code more
-   readable and more like the shell script from whcih someone is
+   readable and more like the shell script from which someone is
    likely porting.
 
 2. Build execution environment
@@ -32,12 +56,14 @@ import sys
 import shutil
 import multiprocessing
 import platform
+
+import llnl.util.tty as tty
 from llnl.util.filesystem import *
 
 import spack
-import spack.compilers as compilers
-from spack.util.executable import Executable, which
+from spack.environment import EnvironmentModifications, validate
 from spack.util.environment import *
+from spack.util.executable import Executable, which
 
 #
 # This can be set by the user to globally disable parallel builds.
@@ -58,6 +84,11 @@ SPACK_SHORT_SPEC       = 'SPACK_SHORT_SPEC'
 SPACK_DEBUG_LOG_DIR    = 'SPACK_DEBUG_LOG_DIR'
 
 
+# Platform-specific library suffix.
+dso_suffix = 'dylib' if sys.platform == 'darwin' else 'so'
+
+
+
 class MakeExecutable(Executable):
     """Special callable executable object for make so the user can
        specify parallel or not on a per-invocation basis.  Using
@@ -146,99 +177,125 @@ def get_path_from_module(mod):
 def set_compiler_environment_variables(pkg):
     assert(pkg.spec.concrete)
     compiler = pkg.compiler
+    flags = pkg.spec.compiler_flags
 
     # Set compiler variables used by CMake and autotools
-    assert all(key in pkg.compiler.link_paths
-               for key in ('cc', 'cxx', 'f77', 'fc'))
+    assert all(key in compiler.link_paths for key in ('cc', 'cxx', 'f77', 'fc'))
 
+    # Populate an object with the list of environment modifications
+    # and return it
+    # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc.
     link_dir = spack.build_env_path
-    os.environ['CC']  = join_path(link_dir, pkg.compiler.link_paths['cc'])
-    os.environ['CXX'] = join_path(link_dir, pkg.compiler.link_paths['cxx'])
-    os.environ['F77'] = join_path(link_dir, pkg.compiler.link_paths['f77'])
-    os.environ['FC']  = join_path(link_dir, pkg.compiler.link_paths['fc'])
+    env.set('CC',  join_path(link_dir, compiler.link_paths['cc']))
+    env.set('CXX', join_path(link_dir, compiler.link_paths['cxx']))
+    env.set('F77', join_path(link_dir, compiler.link_paths['f77']))
+    env.set('FC',  join_path(link_dir, compiler.link_paths['fc']))
 
     # Set SPACK compiler variables so that our wrapper knows what to call
     if compiler.cc:
-        os.environ['SPACK_CC']  = compiler.cc
+        env.set('SPACK_CC', compiler.cc)
     if compiler.cxx:
-        os.environ['SPACK_CXX'] = compiler.cxx
+        env.set('SPACK_CXX', compiler.cxx)
     if compiler.f77:
-        os.environ['SPACK_F77'] = compiler.f77
+        env.set('SPACK_F77', compiler.f77)
     if compiler.fc:
-        os.environ['SPACK_FC']  = compiler.fc
-
-    os.environ['SPACK_COMPILER_SPEC']  = str(pkg.spec.compiler)
-
+        env.set('SPACK_FC',  compiler.fc)
+
+    # Set SPACK compiler rpath flags so that our wrapper knows what to use
+    env.set('SPACK_CC_RPATH_ARG',  compiler.cc_rpath_arg)
+    env.set('SPACK_CXX_RPATH_ARG', compiler.cxx_rpath_arg)
+    env.set('SPACK_F77_RPATH_ARG', compiler.f77_rpath_arg)
+    env.set('SPACK_FC_RPATH_ARG',  compiler.fc_rpath_arg)
+
+    # Add every valid compiler flag to the environment, prefixed with "SPACK_"
+    for flag in spack.spec.FlagMap.valid_compiler_flags():
+        # Concreteness guarantees key safety here
+        if flags[flag] != []:
+            env.set('SPACK_' + flag.upper(), ' '.join(f for f in flags[flag]))
+
+#ifdef NEW
+    env.set('SPACK_COMPILER_SPEC', str(pkg.spec.compiler))
+    return env
+#else /* not NEW */
     for mod in compiler.modules:
         load_module(mod)
+#endif /* not NEW */
 
-def set_build_environment_variables(pkg):
-    """This ensures a clean install environment when we build packages.
+
+def set_build_environment_variables(pkg, env):
+    """
+    This ensures a clean install environment when we build packages
     """
     # Add spack build environment path with compiler wrappers first in
     # the path. We add both spack.env_path, which includes default
     # wrappers (cc, c++, f77, f90), AND a subdirectory containing
     # compiler-specific symlinks.  The latter ensures that builds that
     # are sensitive to the *name* of the compiler see the right name
-    # when we're building wtih the wrappers.
+    # when we're building with the wrappers.
     #
     # Conflicts on case-insensitive systems (like "CC" and "cc") are
     # handled by putting one in the <build_env_path>/case-insensitive
     # directory.  Add that to the path too.
     env_paths = []
-    def add_env_path(path):
-        env_paths.append(path)
-        ci = join_path(path, 'case-insensitive')
-        if os.path.isdir(ci): env_paths.append(ci)
-    add_env_path(spack.build_env_path)
-    add_env_path(join_path(spack.build_env_path, pkg.compiler.name))
-
-    path_put_first("PATH", env_paths)
-    path_set(SPACK_ENV_PATH, env_paths)
-
-    # Prefixes of all of the package's dependencies go in
-    # SPACK_DEPENDENCIES
+    for item in [spack.build_env_path, join_path(spack.build_env_path, pkg.compiler.name)]:
+        env_paths.append(item)
+        ci = join_path(item, 'case-insensitive')
+        if os.path.isdir(ci):
+            env_paths.append(ci)
+
+    for item in reversed(env_paths):
+        env.prepend_path('PATH', item)
+    env.set_path(SPACK_ENV_PATH, env_paths)
+
+    # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES
     dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)]
-    path_set(SPACK_DEPENDENCIES, dep_prefixes)
+    env.set_path(SPACK_DEPENDENCIES, dep_prefixes)
+    env.set_path('CMAKE_PREFIX_PATH', dep_prefixes)  # Add dependencies to CMAKE_PREFIX_PATH
 
     # Install prefix
-    os.environ[SPACK_PREFIX] = pkg.prefix
+    env.set(SPACK_PREFIX, pkg.prefix)
 
     # Install root prefix
-    os.environ[SPACK_INSTALL] = spack.install_path
+    env.set(SPACK_INSTALL, spack.install_path)
 
     # Remove these vars from the environment during build because they
     # can affect how some packages find libraries.  We want to make
     # sure that builds never pull in unintended external dependencies.
-    pop_keys(os.environ, "LD_LIBRARY_PATH", "LD_RUN_PATH", "DYLD_LIBRARY_PATH")
+    env.unset('LD_LIBRARY_PATH')
+    env.unset('LD_RUN_PATH')
+    env.unset('DYLD_LIBRARY_PATH')
 
     # Add bin directories from dependencies to the PATH for the build.
-    bin_dirs = ['%s/bin' % prefix for prefix in dep_prefixes]
-    path_put_first('PATH', [bin for bin in bin_dirs if os.path.isdir(bin)])
+    bin_dirs = reversed(filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes]))
+    for item in bin_dirs:
+        env.prepend_path('PATH', item)
 
     # Working directory for the spack command itself, for debug logs.
     if spack.debug:
-        os.environ[SPACK_DEBUG] = "TRUE"
-    os.environ[SPACK_SHORT_SPEC] = pkg.spec.short_spec
-    os.environ[SPACK_DEBUG_LOG_DIR] = spack.spack_working_dir
-
-    # Add dependencies to CMAKE_PREFIX_PATH
-    path_set("CMAKE_PREFIX_PATH", dep_prefixes)
+        env.set(SPACK_DEBUG, 'TRUE')
+    env.set(SPACK_SHORT_SPEC, pkg.spec.short_spec)
+    env.set(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir)
 
     # Add any pkgconfig directories to PKG_CONFIG_PATH
     pkg_config_dirs = []
     for p in dep_prefixes:
-        for libdir in ('lib', 'lib64'):
-            pcdir = join_path(p, libdir, 'pkgconfig')
+        for maybe in ('lib', 'lib64', 'share'):
+            pcdir = join_path(p, maybe, 'pkgconfig')
             if os.path.isdir(pcdir):
                 pkg_config_dirs.append(pcdir)
+#ifdef NEW
+    env.set_path('PKG_CONFIG_PATH', pkg_config_dirs)
+
+    return env
+#else /* not NEW */
     path_put_first("PKG_CONFIG_PATH", pkg_config_dirs)
 
     if pkg.spec.architecture.target.module_name:
         load_module(pkg.spec.architecture.target.module_name)
+#endif /* not NEW */
 
 
-def set_module_variables_for_package(pkg, m):
+def set_module_variables_for_package(pkg, module):
     """Populate the module scope of install() with some useful functions.
        This makes things easier for package writers.
     """
@@ -248,6 +305,8 @@ def set_module_variables_for_package(pkg, m):
         jobs = 1
     elif pkg.make_jobs:
         jobs = pkg.make_jobs
+
+    m = module
     m.make_jobs = jobs
 
     # TODO: make these build deps that can be installed if not found.
@@ -265,7 +324,7 @@ def set_module_variables_for_package(pkg, m):
     # TODO: of build dependencies, as opposed to link dependencies.
     # TODO: Currently, everything is a link dependency, but tools like
     # TODO: this shouldn't be.
-    m.cmake = which("cmake")
+    m.cmake = Executable('cmake')
 
     # standard CMake arguments
     m.std_cmake_args = ['-DCMAKE_INSTALL_PREFIX=%s' % pkg.prefix,
@@ -282,7 +341,7 @@ def set_module_variables_for_package(pkg, m):
     m.spack_cc  = join_path(link_dir, pkg.compiler.link_paths['cc'])
     m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx'])
     m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77'])
-    m.spack_f90 = join_path(link_dir, pkg.compiler.link_paths['fc'])
+    m.spack_fc  = join_path(link_dir, pkg.compiler.link_paths['fc'])
 
     # Emulate some shell commands for convenience
     m.pwd          = os.getcwd
@@ -303,6 +362,9 @@ def set_module_variables_for_package(pkg, m):
     # a Prefix object.
     m.prefix  = pkg.prefix
 
+    # Platform-specific library suffix.
+    m.dso_suffix = dso_suffix
+
 
 def get_rpaths(pkg):
     """Get a list of all the rpaths for a package."""
@@ -334,22 +396,53 @@ def parent_class_modules(cls):
 
 def setup_package(pkg):
     """Execute all environment setup routines."""
-    set_compiler_environment_variables(pkg)
-    set_build_environment_variables(pkg)
-
-    # If a user makes their own package repo, e.g.
-    # spack.repos.mystuff.libelf.Libelf, and they inherit from
-    # an existing class like spack.repos.original.libelf.Libelf,
-    # then set the module variables for both classes so the
-    # parent class can still use them if it gets called.
-    modules = parent_class_modules(pkg.__class__)
-    for mod in modules:
-        set_module_variables_for_package(pkg, mod)
+    spack_env = EnvironmentModifications()
+    run_env   = EnvironmentModifications()
 
-    # Allow dependencies to set up environment as well.
-    for dep_spec in pkg.spec.traverse(root=False):
-        dep_spec.package.setup_dependent_environment(
-            pkg.module, dep_spec, pkg.spec)
+    # Before proceeding, ensure that specs and packages are consistent
+    #
+    # This is a confusing behavior due to how packages are
+    # constructed.  `setup_dependent_package` may set attributes on
+    # specs in the DAG for use by other packages' install
+    # method. However, spec.package will look up a package via
+    # spack.repo, which defensively copies specs into packages.  This
+    # code ensures that all packages in the DAG have pieces of the
+    # same spec object at build time.
+    #
+    # This is safe for the build process, b/c the build process is a
+    # throwaway environment, but it is kind of dirty.
+    #
+    # TODO: Think about how to avoid this fix and do something cleaner.
+    for s in pkg.spec.traverse(): s.package.spec = s
+
+    set_compiler_environment_variables(pkg, spack_env)
+    set_build_environment_variables(pkg, spack_env)
+
+    # traverse in postorder so package can use vars from its dependencies
+    spec = pkg.spec
+    for dspec in pkg.spec.traverse(order='post', root=False):
+        # If a user makes their own package repo, e.g.
+        # spack.repos.mystuff.libelf.Libelf, and they inherit from
+        # an existing class like spack.repos.original.libelf.Libelf,
+        # then set the module variables for both classes so the
+        # parent class can still use them if it gets called.
+        spkg = dspec.package
+        modules = parent_class_modules(spkg.__class__)
+        for mod in modules:
+            set_module_variables_for_package(spkg, mod)
+        set_module_variables_for_package(spkg, spkg.module)
+
+        # Allow dependencies to modify the module
+        dpkg = dspec.package
+        dpkg.setup_dependent_package(pkg.module, spec)
+        dpkg.setup_dependent_environment(spack_env, run_env, spec)
+
+    set_module_variables_for_package(pkg, pkg.module)
+    pkg.setup_environment(spack_env, run_env)
+
+    # Make sure nothing's strange about the Spack environment.
+    validate(spack_env, tty.warn)
+    spack_env.apply_modifications()
 
 
 def fork(pkg, function):
@@ -366,23 +459,23 @@ def fork(pkg, function):
            # do stuff
        build_env.fork(pkg, child_fun)
 
-    Forked processes are run with the build environemnt set up by
+    Forked processes are run with the build environment set up by
     spack.build_environment.  This allows package authors to have
-    full control over the environment, etc. without offecting
+    full control over the environment, etc. without affecting
     other builds that might be executed in the same spack call.
 
-    If something goes wrong, the child process is expected toprint
+    If something goes wrong, the child process is expected to print
     the error and the parent process will exit with error as
     well. If things go well, the child exits and the parent
     carries on.
     """
     try:
         pid = os.fork()
-    except OSError, e:
+    except OSError as e:
         raise InstallError("Unable to fork build process: %s" % e)
 
     if pid == 0:
-        # Give the child process the package's build environemnt.
+        # Give the child process the package's build environment.
         setup_package(pkg)
 
         try:
@@ -393,7 +486,7 @@ def fork(pkg, function):
             # which interferes with unit tests.
             os._exit(0)
 
-        except spack.error.SpackError, e:
+        except spack.error.SpackError as e:
             e.die()
 
         except:
@@ -408,8 +501,7 @@ def fork(pkg, function):
         # message.  Just make the parent exit with an error code.
         pid, returncode = os.waitpid(pid, 0)
         if returncode != 0:
-            raise InstallError("Installation process had nonzero exit code."
-                .format(str(returncode)))
+            raise InstallError("Installation process had nonzero exit code.".format(str(returncode)))
 
 
 class InstallError(spack.error.SpackError):
diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index 6c635a1e6c..672999159c 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re
diff --git a/lib/spack/spack/cmd/activate.py b/lib/spack/spack/cmd/activate.py
index bcd01f2a28..9867fa8835 100644
--- a/lib/spack/spack/cmd/activate.py
+++ b/lib/spack/spack/cmd/activate.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import llnl.util.tty as tty
diff --git a/lib/spack/spack/cmd/arch.py b/lib/spack/spack/cmd/arch.py
index cd0ce2bb2e..cf2f96fd21 100644
--- a/lib/spack/spack/cmd/arch.py
+++ b/lib/spack/spack/cmd/arch.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack
 import spack.architecture as architecture
diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py
index bdbd623b39..bec11439b5 100644
--- a/lib/spack/spack/cmd/bootstrap.py
+++ b/lib/spack/spack/cmd/bootstrap.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 from subprocess import check_call
diff --git a/lib/spack/spack/cmd/cd.py b/lib/spack/spack/cmd/cd.py
index 16cbe6555a..aa45f67ae1 100644
--- a/lib/spack/spack/cmd/cd.py
+++ b/lib/spack/spack/cmd/cd.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack.cmd.location
 import spack.modules
diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py
index 518d2703dc..95bd4771ed 100644
--- a/lib/spack/spack/cmd/checksum.py
+++ b/lib/spack/spack/cmd/checksum.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import hashlib
diff --git a/lib/spack/spack/cmd/clean.py b/lib/spack/spack/cmd/clean.py
index 6e7179122c..514c5874ef 100644
--- a/lib/spack/spack/cmd/clean.py
+++ b/lib/spack/spack/cmd/clean.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 
diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index e3d311b6b8..030aa77c30 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -1,54 +1,52 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+import argparse
 import sys
-from external import argparse
 
 import llnl.util.tty as tty
-from llnl.util.tty.color import colorize
-from llnl.util.tty.colify import colify
-from llnl.util.lang import index_by
-
-import spack.architecture
-import spack.compiler
 import spack.compilers
-import spack.spec
 import spack.config
-from spack.util.environment import get_path
+import spack.spec
+from llnl.util.lang import index_by
+from llnl.util.tty.colify import colify
+from llnl.util.tty.color import colorize
 from spack.spec import CompilerSpec
+from spack.util.environment import get_path
 
 description = "Manage compilers"
 
 def setup_parser(subparser):
-    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='compiler_command')
+    sp = subparser.add_subparsers(
+        metavar='SUBCOMMAND', dest='compiler_command')
 
     scopes = spack.config.config_scopes
 
-    # Add
-    add_parser = sp.add_parser('add', help='Add compilers to the Spack configuration.')
-    add_parser.add_argument('add_paths', nargs=argparse.REMAINDER)
-    add_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+    # Find
+    find_parser = sp.add_parser('find', aliases=['add'], help='Search the system for compilers to add to the Spack configuration.')
+    find_parser.add_argument('add_paths', nargs=argparse.REMAINDER)
+    find_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope,
                             help="Configuration scope to modify.")
 
     # Remove
@@ -74,13 +72,11 @@ def setup_parser(subparser):
 def compiler_add(args):
     """Search either $PATH or a list of paths OR MODULES for compilers and add them
        to Spack's configuration."""
-
-
-    paths = args.add_paths # This might be a parser method. Parsing method to add_paths
+    paths = args.add_paths
     if not paths:
         paths = get_path('PATH')
 
-    compilers = [c for c in spack.compilers.find_compilers(*paths)
+    compilers = [c for c in spack.compilers.find_compilers(*args.add_paths)
                  if c.spec not in spack.compilers.all_compilers(scope=args.scope)]
 
     if compilers:
diff --git a/lib/spack/spack/cmd/compilers.py b/lib/spack/spack/cmd/compilers.py
index 7e09016f2d..9fbc2bb952 100644
--- a/lib/spack/spack/cmd/compilers.py
+++ b/lib/spack/spack/cmd/compilers.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
diff --git a/lib/spack/spack/cmd/config.py b/lib/spack/spack/cmd/config.py
index 5e6d4e4d7d..d6f56c270d 100644
--- a/lib/spack/spack/cmd/config.py
+++ b/lib/spack/spack/cmd/config.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import argparse
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index 4564143f83..41bfa741f6 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -1,27 +1,29 @@
+_copyright = """\
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+"""
 import string
 import os
 import hashlib
@@ -47,22 +49,22 @@ from spack.stage import Stage
 
 description = "Create a new package file from an archive URL"
 
-package_template = string.Template("""\
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
+package_template = string.Template(
+    _copyright + """
 #
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
+# This is a template package file for Spack.  We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
 #
 #     spack install ${name}
 #
-# You can always get back here to change things with:
+# You can edit this file again by typing:
 #
 #     spack edit ${name}
 #
-# See the spack documentation for more information on building
-# packages.
+# See the Spack documentation for more information on packaging.
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
 #
 from spack import *
 
@@ -124,10 +126,12 @@ class ConfigureGuesser(object):
         autotools = "configure('--prefix=%s' % prefix)"
         cmake     = "cmake('.', *std_cmake_args)"
         python    = "python('setup.py', 'install', '--prefix=%s' % prefix)"
+        r         = "R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)"
 
         config_lines = ((r'/configure$',      'autotools', autotools),
                         (r'/CMakeLists.txt$', 'cmake',     cmake),
-                        (r'/setup.py$',       'python',    python))
+                        (r'/setup.py$',       'python',    python),
+                        (r'/NAMESPACE$',      'r',         r))
 
         # Peek inside the tarball.
         tar = which('tar')
@@ -208,7 +212,7 @@ def find_repository(spec, args):
     return repo
 
 
-def fetch_tarballs(url, name, args):
+def fetch_tarballs(url, name, version):
     """Try to find versions of the supplied archive by scraping the web.
 
     Prompts the user to select how many to download if many are found.
@@ -222,7 +226,7 @@ def fetch_tarballs(url, name, args):
     archives_to_fetch = 1
     if not versions:
         # If the fetch failed for some reason, revert to what the user provided
-        versions = { "version" : url }
+        versions = { version : url }
     elif len(versions) > 1:
         tty.msg("Found %s versions of %s:" % (len(versions), name),
                 *spack.cmd.elide_list(
@@ -256,7 +260,7 @@ def create(parser, args):
     tty.msg("Creating template for package %s" % name)
 
     # Fetch tarballs (prompting user if necessary)
-    versions, urls = fetch_tarballs(url, name, args)
+    versions, urls = fetch_tarballs(url, name, version)
 
     # Try to guess what configure system is used.
     guesser = ConfigureGuesser()
@@ -272,6 +276,10 @@ def create(parser, args):
     if guesser.build_system == 'python':
         name = 'py-%s' % name
 
+    # Prepend 'r-' to R package names, by convention.
+    if guesser.build_system == 'r':
+        name = 'r-%s' % name
+
     # Create a directory for the new package.
     pkg_path = repo.filename_for_package_name(name)
     if os.path.exists(pkg_path) and not args.force:
diff --git a/lib/spack/spack/cmd/deactivate.py b/lib/spack/spack/cmd/deactivate.py
index d6b23d6a08..990309ee48 100644
--- a/lib/spack/spack/cmd/deactivate.py
+++ b/lib/spack/spack/cmd/deactivate.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import llnl.util.tty as tty
diff --git a/lib/spack/spack/cmd/dependents.py b/lib/spack/spack/cmd/dependents.py
index de76098d2f..78eb6847b8 100644
--- a/lib/spack/spack/cmd/dependents.py
+++ b/lib/spack/spack/cmd/dependents.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 
diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py
index 2c3a8761ab..39faf59a17 100644
--- a/lib/spack/spack/cmd/diy.py
+++ b/lib/spack/spack/cmd/diy.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import os
@@ -75,8 +75,8 @@ def diy(self, args):
                 edit_package(spec.name, spack.repo.first_repo(), None, True)
                 return
 
-        if not spec.version.concrete:
-            tty.die("spack diy spec must have a single, concrete version.")
+        if not spec.versions.concrete:
+            tty.die("spack diy spec must have a single, concrete version.  Did you forget a package version number?")
 
         spec.concretize()
         package = spack.repo.get(spec)
diff --git a/lib/spack/spack/cmd/doc.py b/lib/spack/spack/cmd/doc.py
index 29cadec94f..b3d0737d13 100644
--- a/lib/spack/spack/cmd/doc.py
+++ b/lib/spack/spack/cmd/doc.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 description = "Run pydoc from within spack."
diff --git a/lib/spack/spack/cmd/edit.py b/lib/spack/spack/cmd/edit.py
index a20e40df9b..49ab83867a 100644
--- a/lib/spack/spack/cmd/edit.py
+++ b/lib/spack/spack/cmd/edit.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import string
diff --git a/lib/spack/spack/cmd/env.py b/lib/spack/spack/cmd/env.py
index 525e955a00..85d111e91e 100644
--- a/lib/spack/spack/cmd/env.py
+++ b/lib/spack/spack/cmd/env.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import argparse
diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
index ccb0fe4e1f..11659e0c96 100644
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import argparse
diff --git a/lib/spack/spack/cmd/fetch.py b/lib/spack/spack/cmd/fetch.py
index adad545cae..e40caaa234 100644
--- a/lib/spack/spack/cmd/fetch.py
+++ b/lib/spack/spack/cmd/fetch.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 
diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index 95f035c7bf..c768faea91 100644
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -1,78 +1,114 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
-import collections
-import itertools
 import argparse
-from StringIO import StringIO
+import sys
 
 import llnl.util.tty as tty
+import spack
+import spack.spec
+from llnl.util.lang import *
 from llnl.util.tty.colify import *
 from llnl.util.tty.color import *
 from llnl.util.lang import *
 
-import spack
-import spack.spec
+description = "Find installed spack packages"
 
-description ="Find installed spack packages"
 
 def setup_parser(subparser):
     format_group = subparser.add_mutually_exclusive_group()
+    format_group.add_argument('-s',
+                              '--short',
+                              action='store_const',
+                              dest='mode',
+                              const='short',
+                              help='Show only specs (default)')
+    format_group.add_argument('-p',
+                              '--paths',
+                              action='store_const',
+                              dest='mode',
+                              const='paths',
+                              help='Show paths to package install directories')
     format_group.add_argument(
-        '-s', '--short', action='store_const', dest='mode', const='short',
-        help='Show only specs (default)')
-    format_group.add_argument(
-        '-p', '--paths', action='store_const', dest='mode', const='paths',
-        help='Show paths to package install directories')
-    format_group.add_argument(
-        '-d', '--deps', action='store_const', dest='mode', const='deps',
+        '-d',
+        '--deps',
+        action='store_const',
+        dest='mode',
+        const='deps',
         help='Show full dependency DAG of installed packages')
 
+    subparser.add_argument('-l',
+                           '--long',
+                           action='store_true',
+                           dest='long',
+                           help='Show dependency hashes as well as versions.')
+    subparser.add_argument('-L',
+                           '--very-long',
+                           action='store_true',
+                           dest='very_long',
+                           help='Show dependency hashes as well as versions.')
+    subparser.add_argument('-f',
+                           '--show-flags',
+                           action='store_true',
+                           dest='show_flags',
+                           help='Show spec compiler flags.')
+
     subparser.add_argument(
-        '-l', '--long', action='store_true',
-        help='Show dependency hashes as well as versions.')
+        '-e',
+        '--explicit',
+        action='store_true',
+        help='Show only specs that were installed explicitly')
     subparser.add_argument(
-        '-L', '--very-long', action='store_true',
-        help='Show dependency hashes as well as versions.')
-
+        '-E',
+        '--implicit',
+        action='store_true',
+        help='Show only specs that were installed as dependencies')
     subparser.add_argument(
-        '-u', '--unknown', action='store_true',
+        '-u',
+        '--unknown',
+        action='store_true',
+        dest='unknown',
         help='Show only specs Spack does not have a package for.')
     subparser.add_argument(
-        '-m', '--missing', action='store_true',
+        '-m',
+        '--missing',
+        action='store_true',
+        dest='missing',
         help='Show missing dependencies as well as installed specs.')
-    subparser.add_argument(
-        '-M', '--only-missing', action='store_true',
-        help='Show only missing dependencies.')
-    subparser.add_argument(
-        '-N', '--namespace', action='store_true',
-        help='Show fully qualified package names.')
+    subparser.add_argument('-M',
+                           '--only-missing',
+                           action='store_true',
+                           dest='only_missing',
+                           help='Show only missing dependencies.')
+    subparser.add_argument('-N',
+                           '--namespace',
+                           action='store_true',
+                           help='Show fully qualified package names.')
 
-    subparser.add_argument(
-        'query_specs', nargs=argparse.REMAINDER,
-        help='optional specs to filter results')
+    subparser.add_argument('query_specs',
+                           nargs=argparse.REMAINDER,
+                           help='optional specs to filter results')
 
 
 def gray_hash(spec, length):
@@ -89,31 +125,29 @@ def display_specs(specs, **kwargs):
         hashes = True
         hlen = None
 
-    # Make a dict with specs keyed by target and compiler.
-    index = index_by(specs, ('architecture', 'compiler'))
-
-    # Create sort key based off of whether read architecture is string
-    def sort_key(index_dict):
-        if isinstance(index_dict[0],basestring):
-            return(str, index_dict[1]._cmp_key())
-        elif isinstance(index_dict[0], spack.architecture.Arch):
-            return (index_dict[0]._cmp_key(), index_dict[1]._cmp_key())
+    nfmt = '.' if namespace else '_'
+    format_string = '$%s$@$+' % nfmt
+    flags = kwargs.get('show_flags', False)
+    if flags:
+        format_string = '$%s$@$%%+$+' % nfmt
 
-    sorted_index = sorted(index, key=sort_key)
+    # Make a dict with specs keyed by architecture and compiler.
+    index = index_by(specs, ('architecture', 'compiler'))
 
-    for i, (architecture, compiler) in enumerate(sorted_index):
-        if i > 0: print
+    # Traverse the index and print out each package
+    for i, (architecture, compiler) in enumerate(sorted(index)):
+        if i > 0:
+            print
 
-        header = "%s{%s} / %s{%s}" % (
-            spack.spec.architecture_color, architecture,
-            spack.spec.compiler_color, compiler)
+        header = "%s{%s} / %s{%s}" % (spack.spec.architecture_color,
+                                      architecture, spack.spec.compiler_color,
+                                      compiler)
         tty.hline(colorize(header), char='-')
 
         specs = index[(architecture, compiler)]
         specs.sort()
 
-        nfmt = '.' if namespace else '_'
-        abbreviated = [s.format('$%s$@$+' % nfmt, color=True) for s in specs]
+        abbreviated = [s.format(format_string, color=True) for s in specs]
         if mode == 'paths':
             # Print one spec per line along with prefix path
             width = max(len(s) for s in abbreviated)
@@ -122,38 +156,46 @@ def display_specs(specs, **kwargs):
 
             for abbrv, spec in zip(abbreviated, specs):
                 if hashes:
-                    print gray_hash(spec, hlen),
-                print format % (abbrv, spec.prefix)
+                    print(gray_hash(spec, hlen), )
+                print(format % (abbrv, spec.prefix))
 
         elif mode == 'deps':
             for spec in specs:
-                print spec.tree(
-                    format='$%s$@$+' % nfmt,
+                print(spec.tree(
+                    format=format_string,
                     color=True,
                     indent=4,
-                    prefix=(lambda s: gray_hash(s, hlen)) if hashes else None)
+                    prefix=(lambda s: gray_hash(s, hlen)) if hashes else None))
 
         elif mode == 'short':
-            def fmt(s):
-                string = ""
-                if hashes:
-                    string += gray_hash(s, hlen) + ' '
-                string += s.format('$-%s$@$+' % nfmt, color=True)
+            # Print columns of output if not printing flags
+            if not flags:
 
-                return string
-            colify(fmt(s) for s in specs)
+                def fmt(s):
+                    string = ""
+                    if hashes:
+                        string += gray_hash(s, hlen) + ' '
+                    string += s.format('$-%s$@$+' % nfmt, color=True)
 
-        else:
-            raise ValueError(
-                "Invalid mode for display_specs: %s. Must be one of (paths, deps, short)." % mode)
+                    return string
+
+                colify(fmt(s) for s in specs)
+            # Print one entry per line if including flags
+            else:
+                for spec in specs:
+                    # Print the hash if necessary
+                    hsh = gray_hash(spec, hlen) + ' ' if hashes else ''
+                    print(hsh + spec.format(format_string, color=True) + '\n')
 
+        else:
+            raise ValueError("Invalid mode for display_specs: %s. Must be one of (paths, deps, short)." % mode)  # NOQA: ignore=E501
 
 
 def find(parser, args):
     # Filter out specs that don't exist.
     query_specs = spack.cmd.parse_specs(args.query_specs)
     query_specs, nonexisting = partition_list(
-        query_specs, lambda s: spack.repo.exists(s.name))
+        query_specs, lambda s: spack.repo.exists(s.name) or not s.name)
 
     if nonexisting:
         msg = "No such package%s: " % ('s' if len(nonexisting) > 1 else '')
@@ -171,13 +213,21 @@ def find(parser, args):
         installed = any
     if args.unknown:
         known = False
-    q_args = { 'installed' : installed, 'known' : known }
+
+    explicit = any
+    if args.explicit:
+        explicit = False
+    if args.implicit:
+        explicit = True
+
+    q_args = {'installed': installed, 'known': known, "explicit": explicit}
 
     # Get all the specs the user asked for
     if not query_specs:
         specs = set(spack.installed_db.query(**q_args))
     else:
-        results = [set(spack.installed_db.query(qs, **q_args)) for qs in query_specs]
+        results = [set(spack.installed_db.query(qs, **q_args))
+                   for qs in query_specs]
         specs = set.union(*results)
 
     if not args.mode:
@@ -185,7 +235,12 @@ def find(parser, args):
 
     if sys.stdout.isatty():
         tty.msg("%d installed packages." % len(specs))
-    display_specs(specs, mode=args.mode,
+    display_specs(specs,
+                  mode=args.mode,
                   long=args.long,
                   very_long=args.very_long,
+#ifdef NEW
+                  show_flags=args.show_flags)
+#else /* not NEW */
                   namespace=args.namespace)
+#endif /* not NEW */
diff --git a/lib/spack/spack/cmd/graph.py b/lib/spack/spack/cmd/graph.py
index 586a852351..da65121836 100644
--- a/lib/spack/spack/cmd/graph.py
+++ b/lib/spack/spack/cmd/graph.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 
diff --git a/lib/spack/spack/cmd/help.py b/lib/spack/spack/cmd/help.py
index 841a0d5bcb..1d23161839 100644
--- a/lib/spack/spack/cmd/help.py
+++ b/lib/spack/spack/cmd/help.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 
diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py
index e7abe7f4a5..64d0d20e24 100644
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import textwrap
 from llnl.util.tty.colify import *
@@ -52,7 +52,7 @@ def print_text_info(pkg):
     print "Safe versions:  "
 
     if not pkg.versions:
-        print("None")
+        print("    None")
     else:
         pad = padder(pkg.versions, 4)
         for v in reversed(sorted(pkg.versions)):
@@ -62,7 +62,7 @@ def print_text_info(pkg):
     print
     print "Variants:"
     if not pkg.variants:
-        print "None"
+        print "    None"
     else:
         pad = padder(pkg.variants, 4)
 
diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py
index 1fef750c80..9d3175786b 100644
--- a/lib/spack/spack/cmd/install.py
+++ b/lib/spack/spack/cmd/install.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 
@@ -78,4 +78,5 @@ def install(parser, args):
                 ignore_deps=args.ignore_deps,
                 make_jobs=args.jobs,
                 verbose=args.verbose,
-                fake=args.fake)
+                fake=args.fake,
+                explicit=True)
diff --git a/lib/spack/spack/cmd/list.py b/lib/spack/spack/cmd/list.py
index 7c50ccb9cd..1e3699cee0 100644
--- a/lib/spack/spack/cmd/list.py
+++ b/lib/spack/spack/cmd/list.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import llnl.util.tty as tty
diff --git a/lib/spack/spack/cmd/load.py b/lib/spack/spack/cmd/load.py
index 30d86c3b01..54cf01eb43 100644
--- a/lib/spack/spack/cmd/load.py
+++ b/lib/spack/spack/cmd/load.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.modules
diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py
index 307ee8982d..b0dbb1a550 100644
--- a/lib/spack/spack/cmd/location.py
+++ b/lib/spack/spack/cmd/location.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys
diff --git a/lib/spack/spack/cmd/md5.py b/lib/spack/spack/cmd/md5.py
index f99fc0f8c2..3ba3c71562 100644
--- a/lib/spack/spack/cmd/md5.py
+++ b/lib/spack/spack/cmd/md5.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import hashlib
diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py
index fcd15a6a90..d5f7abe212 100644
--- a/lib/spack/spack/cmd/mirror.py
+++ b/lib/spack/spack/cmd/mirror.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys
diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index 1d6867c1d9..5292d42225 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -1,54 +1,52 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
 import os
 import shutil
-import argparse
+import sys
 
 import llnl.util.tty as tty
-from llnl.util.lang import partition_list
-from llnl.util.filesystem import mkdirp
-
 import spack.cmd
+from llnl.util.filesystem import mkdirp
 from spack.modules import module_types
 from spack.util.string import *
 
-from spack.spec import Spec
-
-description ="Manipulate modules and dotkits."
+description = "Manipulate modules and dotkits."
 
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command')
 
-    refresh_parser = sp.add_parser('refresh', help='Regenerate all module files.')
+    sp.add_parser('refresh', help='Regenerate all module files.')
 
     find_parser = sp.add_parser('find', help='Find module files for packages.')
-    find_parser.add_argument(
-        'module_type', help="Type of module to find file for. [" + '|'.join(module_types) + "]")
-    find_parser.add_argument('spec', nargs='+', help='spec to find a module file for.')
+    find_parser.add_argument('module_type',
+                             help="Type of module to find file for. [" +
+                             '|'.join(module_types) + "]")
+    find_parser.add_argument('spec',
+                             nargs='+',
+                             help='spec to find a module file for.')
 
 
 def module_find(mtype, spec_array):
@@ -58,7 +56,8 @@ def module_find(mtype, spec_array):
        should type to use that package's module.
     """
     if mtype not in module_types:
-        tty.die("Invalid module type: '%s'.  Options are %s" % (mtype, comma_or(module_types)))
+        tty.die("Invalid module type: '%s'.  Options are %s" %
+                (mtype, comma_or(module_types)))
 
     specs = spack.cmd.parse_specs(spec_array)
     if len(specs) > 1:
@@ -80,7 +79,7 @@ def module_find(mtype, spec_array):
     if not os.path.isfile(mod.file_name):
         tty.die("No %s module is installed for %s" % (mtype, spec))
 
-    print mod.use_name
+    print(mod.use_name)
 
 
 def module_refresh():
@@ -94,11 +93,9 @@ def module_refresh():
             shutil.rmtree(cls.path, ignore_errors=False)
         mkdirp(cls.path)
         for spec in specs:
-            tty.debug("   Writing file for %s" % spec)
             cls(spec).write()
 
 
-
 def module(parser, args):
     if args.module_command == 'refresh':
         module_refresh()
diff --git a/lib/spack/spack/cmd/package-list.py b/lib/spack/spack/cmd/package-list.py
index 5e37d5c16b..6c5c4ae8c6 100644
--- a/lib/spack/spack/cmd/package-list.py
+++ b/lib/spack/spack/cmd/package-list.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
 import cgi
diff --git a/lib/spack/spack/cmd/patch.py b/lib/spack/spack/cmd/patch.py
index b04b402738..a5507e42cf 100644
--- a/lib/spack/spack/cmd/patch.py
+++ b/lib/spack/spack/cmd/patch.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 
diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py
index cf478d3763..a24c2759fe 100644
--- a/lib/spack/spack/cmd/pkg.py
+++ b/lib/spack/spack/cmd/pkg.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 
@@ -77,7 +77,8 @@ def get_git():
 
 def list_packages(rev):
     git = get_git()
-    relpath = spack.packages_path[len(spack.prefix + os.path.sep):] + os.path.sep
+    pkgpath = os.path.join(spack.packages_path, 'packages')
+    relpath = pkgpath[len(spack.prefix + os.path.sep):] + os.path.sep
     output = git('ls-tree', '--full-tree', '--name-only', rev, relpath,
                  output=str)
     return sorted(line[len(relpath):] for line in output.split('\n') if line)
diff --git a/lib/spack/spack/cmd/providers.py b/lib/spack/spack/cmd/providers.py
index 49d6ac192a..e9007486d2 100644
--- a/lib/spack/spack/cmd/providers.py
+++ b/lib/spack/spack/cmd/providers.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import argparse
diff --git a/lib/spack/spack/cmd/purge.py b/lib/spack/spack/cmd/purge.py
index d5d7513c46..7b33ef7f69 100644
--- a/lib/spack/spack/cmd/purge.py
+++ b/lib/spack/spack/cmd/purge.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack.stage as stage
 
diff --git a/lib/spack/spack/cmd/python.py b/lib/spack/spack/cmd/python.py
index 5325e8fd9a..59423271b9 100644
--- a/lib/spack/spack/cmd/python.py
+++ b/lib/spack/spack/cmd/python.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys
diff --git a/lib/spack/spack/cmd/reindex.py b/lib/spack/spack/cmd/reindex.py
index 2b30ef8814..93eba7a0f1 100644
--- a/lib/spack/spack/cmd/reindex.py
+++ b/lib/spack/spack/cmd/reindex.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack
diff --git a/lib/spack/spack/cmd/repo.py b/lib/spack/spack/cmd/repo.py
index 87c782000f..399237b169 100644
--- a/lib/spack/spack/cmd/repo.py
+++ b/lib/spack/spack/cmd/repo.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://software.llnl.gov/spack
+# For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re
diff --git a/lib/spack/spack/cmd/restage.py b/lib/spack/spack/cmd/restage.py
index 540c2ef2a5..325d30662f 100644
--- a/lib/spack/spack/cmd/restage.py
+++ b/lib/spack/spack/cmd/restage.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 
diff --git a/lib/spack/spack/cmd/spec.py b/lib/spack/spack/cmd/spec.py
index 43a106ea37..321e3e429b 100644
--- a/lib/spack/spack/cmd/spec.py
+++ b/lib/spack/spack/cmd/spec.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.cmd
diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 5786780efb..61e9c6d9ff 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import argparse
@@ -35,6 +35,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check downloaded packages against checksum")
+    subparser.add_argument(
+        '-p', '--path', dest='path',
+        help="Path to stage package, does not add to spack tree")
 
     subparser.add_argument(
         'specs', nargs=argparse.REMAINDER, help="specs of packages to stage")
@@ -50,4 +53,6 @@ def stage(parser, args):
     specs = spack.cmd.parse_specs(args.specs, concretize=True)
     for spec in specs:
         package = spack.repo.get(spec)
+        if args.path:
+            package.path = args.path
         package.do_stage()
diff --git a/lib/spack/spack/cmd/test-install.py b/lib/spack/spack/cmd/test-install.py
index 656873a2f0..45592a7dda 100644
--- a/lib/spack/spack/cmd/test-install.py
+++ b/lib/spack/spack/cmd/test-install.py
@@ -1,109 +1,128 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
-import xml.etree.ElementTree as ET
-import itertools
-import re
-import os
 import codecs
+import os
+import time
+import xml.dom.minidom
+import xml.etree.ElementTree as ET
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import *
-
 import spack
+import spack.cmd
+from llnl.util.filesystem import *
 from spack.build_environment import InstallError
 from spack.fetch_strategy import FetchError
-import spack.cmd
 
 description = "Run package installation as a unit test, output formatted results."
 
-def setup_parser(subparser):
-    subparser.add_argument(
-        '-j', '--jobs', action='store', type=int,
-        help="Explicitly set number of make jobs.  Default is #cpus.")
-
-    subparser.add_argument(
-        '-n', '--no-checksum', action='store_true', dest='no_checksum',
-        help="Do not check packages against checksum")
 
-    subparser.add_argument(
-        '-o', '--output', action='store', help="test output goes in this file")
+def setup_parser(subparser):
+    subparser.add_argument('-j',
+                           '--jobs',
+                           action='store',
+                           type=int,
+                           help="Explicitly set number of make jobs.  Default is #cpus.")
 
-    subparser.add_argument(
-        'package', nargs=argparse.REMAINDER, help="spec of package to install")
+    subparser.add_argument('-n',
+                           '--no-checksum',
+                           action='store_true',
+                           dest='no_checksum',
+                           help="Do not check packages against checksum")
 
+    subparser.add_argument('-o', '--output', action='store', help="test output goes in this file")
 
-class JunitResultFormat(object):
-    def __init__(self):
-        self.root = ET.Element('testsuite')
-        self.tests = []
-
-    def add_test(self, buildId, testResult, buildInfo=None):
-        self.tests.append((buildId, testResult, buildInfo))
-
-    def write_to(self, stream):
-        self.root.set('tests', '{0}'.format(len(self.tests)))
-        for buildId, testResult, buildInfo in self.tests:
-            testcase = ET.SubElement(self.root, 'testcase')
-            testcase.set('classname', buildId.name)
-            testcase.set('name', buildId.stringId())
-            if testResult == TestResult.FAILED:
-                failure = ET.SubElement(testcase, 'failure')
-                failure.set('type', "Build Error")
-                failure.text = buildInfo
-            elif testResult == TestResult.SKIPPED:
-                skipped = ET.SubElement(testcase, 'skipped')
-                skipped.set('type', "Skipped Build")
-                skipped.text = buildInfo
-        ET.ElementTree(self.root).write(stream)
+    subparser.add_argument('package', nargs=argparse.REMAINDER, help="spec of package to install")
 
 
 class TestResult(object):
     PASSED = 0
     FAILED = 1
     SKIPPED = 2
+    ERRORED = 3
 
 
-class BuildId(object):
-    def __init__(self, spec):
-        self.name = spec.name
-        self.version = spec.version
-        self.hashId = spec.dag_hash()
-
-    def stringId(self):
-        return "-".join(str(x) for x in (self.name, self.version, self.hashId))
-
-    def __hash__(self):
-        return hash((self.name, self.version, self.hashId))
-
-    def __eq__(self, other):
-        if not isinstance(other, BuildId):
-            return False
+class TestSuite(object):
+    def __init__(self, filename):
+        self.filename = filename
+        self.root = ET.Element('testsuite')
+        self.tests = []
 
-        return ((self.name, self.version, self.hashId) ==
-            (other.name, other.version, other.hashId))
+    def __enter__(self):
+        return self
+
+    def append(self, item):
+        if not isinstance(item, TestCase):
+            raise TypeError('only TestCase instances may be appended to a TestSuite instance')
+        self.tests.append(item)  # Append the item to the list of tests
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        # Prepare the header for the entire test suite
+        number_of_errors = sum(x.result_type == TestResult.ERRORED for x in self.tests)
+        self.root.set('errors', str(number_of_errors))
+        number_of_failures = sum(x.result_type == TestResult.FAILED for x in self.tests)
+        self.root.set('failures', str(number_of_failures))
+        self.root.set('tests', str(len(self.tests)))
+
+        for item in self.tests:
+            self.root.append(item.element)
+
+        with open(self.filename, 'wb') as file:
+            xml_string = ET.tostring(self.root)
+            xml_string = xml.dom.minidom.parseString(xml_string).toprettyxml()
+            file.write(xml_string)
+
+
+class TestCase(object):
+
+    results = {
+        TestResult.PASSED: None,
+        TestResult.SKIPPED: 'skipped',
+        TestResult.FAILED: 'failure',
+        TestResult.ERRORED: 'error',
+    }
+
+    def __init__(self, classname, name, time=None):
+        self.element = ET.Element('testcase')
+        self.element.set('classname', str(classname))
+        self.element.set('name', str(name))
+        if time is not None:
+            self.element.set('time', str(time))
+        self.result_type = None
+
+    def set_result(self, result_type, message=None, error_type=None, text=None):
+        self.result_type = result_type
+        result = TestCase.results[self.result_type]
+        if result is not None and result is not TestResult.PASSED:
+            subelement = ET.SubElement(self.element, result)
+            if error_type is not None:
+                subelement.set('type', error_type)
+            if message is not None:
+                subelement.set('message', str(message))
+            if text is not None:
+                subelement.text = text
 
 
 def fetch_log(path):
@@ -114,46 +133,76 @@ def fetch_log(path):
 
 
 def failed_dependencies(spec):
-    return set(childSpec for childSpec in spec.dependencies.itervalues() if not
-        spack.repo.get(childSpec).installed)
-
-
-def create_test_output(topSpec, newInstalls, output, getLogFunc=fetch_log):
-    # Post-order traversal is not strictly required but it makes sense to output
-    # tests for dependencies first.
-    for spec in topSpec.traverse(order='post'):
-        if spec not in newInstalls:
-            continue
-
-        failedDeps = failed_dependencies(spec)
-        package = spack.repo.get(spec)
-        if failedDeps:
-            result = TestResult.SKIPPED
-            dep = iter(failedDeps).next()
-            depBID = BuildId(dep)
-            errOutput = "Skipped due to failed dependency: {0}".format(
-                depBID.stringId())
-        elif (not package.installed) and (not package.stage.source_path):
-            result = TestResult.FAILED
-            errOutput = "Failure to fetch package resources."
-        elif not package.installed:
-            result = TestResult.FAILED
-            lines = getLogFunc(package.build_log_path)
-            errMessages = list(line for line in lines if
-                re.search('error:', line, re.IGNORECASE))
-            errOutput = errMessages if errMessages else lines[-10:]
-            errOutput = '\n'.join(itertools.chain(
-                    [spec.to_yaml(), "Errors:"], errOutput,
-                    ["Build Log:", package.build_log_path]))
-        else:
-            result = TestResult.PASSED
-            errOutput = None
-
-        bId = BuildId(spec)
-        output.add_test(bId, result, errOutput)
+    return set(item for item in spec.dependencies.itervalues() if not spack.repo.get(item).installed)
+
+
+def get_top_spec_or_die(args):
+    specs = spack.cmd.parse_specs(args.package, concretize=True)
+    if len(specs) > 1:
+        tty.die("Only 1 top-level package can be specified")
+    top_spec = iter(specs).next()
+    return top_spec
+
+
+def install_single_spec(spec, number_of_jobs):
+    package = spack.repo.get(spec)
+
+    # If it is already installed, skip the test
+    if spack.repo.get(spec).installed:
+        testcase = TestCase(package.name, package.spec.short_spec, time=0.0)
+        testcase.set_result(TestResult.SKIPPED, message='Skipped [already installed]', error_type='already_installed')
+        return testcase
+
+    # If it relies on dependencies that did not install, skip
+    if failed_dependencies(spec):
+        testcase = TestCase(package.name, package.spec.short_spec, time=0.0)
+        testcase.set_result(TestResult.SKIPPED, message='Skipped [failed dependencies]', error_type='dep_failed')
+        return testcase
+
+    # Otherwise try to install the spec
+    try:
+        start_time = time.time()
+        package.do_install(keep_prefix=False,
+                           keep_stage=True,
+                           ignore_deps=False,
+                           make_jobs=number_of_jobs,
+                           verbose=True,
+                           fake=False)
+        duration = time.time() - start_time
+        testcase = TestCase(package.name, package.spec.short_spec, duration)
+        testcase.set_result(TestResult.PASSED)
+    except InstallError:
+        # An InstallError is considered a failure (the recipe didn't work correctly)
+        duration = time.time() - start_time
+        # Try to get the log
+        lines = fetch_log(package.build_log_path)
+        text = '\n'.join(lines)
+        testcase = TestCase(package.name, package.spec.short_spec, duration)
+        testcase.set_result(TestResult.FAILED, message='Installation failure', text=text)
+
+    except FetchError:
+        # A FetchError is considered an error (we didn't even start building)
+        duration = time.time() - start_time
+        testcase = TestCase(package.name, package.spec.short_spec, duration)
+        testcase.set_result(TestResult.ERRORED, message='Unable to fetch package')
+
+    return testcase
+
+
+def get_filename(args, top_spec):
+    if not args.output:
+        fname = 'test-{x.name}-{x.version}-{hash}.xml'.format(x=top_spec, hash=top_spec.dag_hash())
+        output_directory = join_path(os.getcwd(), 'test-output')
+        if not os.path.exists(output_directory):
+            os.mkdir(output_directory)
+        output_filename = join_path(output_directory, fname)
+    else:
+        output_filename = args.output
+    return output_filename
 
 
 def test_install(parser, args):
+    # Check the input
     if not args.package:
         tty.die("install requires a package argument")
 
@@ -162,50 +211,15 @@ def test_install(parser, args):
             tty.die("The -j option must be a positive integer!")
 
     if args.no_checksum:
-        spack.do_checksum = False        # TODO: remove this global.
-
-    specs = spack.cmd.parse_specs(args.package, concretize=True)
-    if len(specs) > 1:
-        tty.die("Only 1 top-level package can be specified")
-    topSpec = iter(specs).next()
-
-    newInstalls = set()
-    for spec in topSpec.traverse():
-        package = spack.repo.get(spec)
-        if not package.installed:
-            newInstalls.add(spec)
-
-    if not args.output:
-        bId = BuildId(topSpec)
-        outputDir = join_path(os.getcwd(), "test-output")
-        if not os.path.exists(outputDir):
-            os.mkdir(outputDir)
-        outputFpath = join_path(outputDir, "test-{0}.xml".format(bId.stringId()))
-    else:
-        outputFpath = args.output
-
-    for spec in topSpec.traverse(order='post'):
-        # Calling do_install for the top-level package would be sufficient but
-        # this attempts to keep going if any package fails (other packages which
-        # are not dependents may succeed)
-        package = spack.repo.get(spec)
-        if (not failed_dependencies(spec)) and (not package.installed):
-            try:
-                package.do_install(
-                    keep_prefix=False,
-                    keep_stage=True,
-                    ignore_deps=False,
-                    make_jobs=args.jobs,
-                    verbose=True,
-                    fake=False)
-            except InstallError:
-                pass
-            except FetchError:
-                pass
-
-    jrf = JunitResultFormat()
-    handled = {}
-    create_test_output(topSpec, newInstalls, jrf)
-
-    with open(outputFpath, 'wb') as F:
-            jrf.write_to(F)
+        spack.do_checksum = False  # TODO: remove this global.
+
+    # Get the one and only top spec
+    top_spec = get_top_spec_or_die(args)
+    # Get the filename of the test
+    output_filename = get_filename(args, top_spec)
+    # TEST SUITE
+    with TestSuite(output_filename) as test_suite:
+        # Traverse in post order : each spec is a test case
+        for spec in top_spec.traverse(order='post'):
+            test_case = install_single_spec(spec, args.jobs)
+            test_suite.append(test_case)
diff --git a/lib/spack/spack/cmd/test.py b/lib/spack/spack/cmd/test.py
index ddc6cb4fce..cb9dd26c71 100644
--- a/lib/spack/spack/cmd/test.py
+++ b/lib/spack/spack/cmd/test.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 from pprint import pprint
diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index d01aa2136b..9fdf3045b2 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -1,40 +1,55 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
+from __future__ import print_function
+
 import argparse
 
 import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
-
 import spack
 import spack.cmd
 import spack.repository
 from spack.cmd.find import display_specs
-from spack.package import PackageStillNeededError
 
-description="Remove an installed package"
+description = "Remove an installed package"
+
+error_message = """You can either:
+    a) Use a more specific spec, or
+    b) use spack uninstall -a to uninstall ALL matching specs.
+"""
+
+
+def ask_for_confirmation(message):
+    while True:
+        tty.msg(message + '[y/n]')
+        choice = raw_input().lower()
+        if choice == 'y':
+            break
+        elif choice == 'n':
+            raise SystemExit('Operation aborted')
+        tty.warn('Please reply either "y" or "n"')
+
 
 def setup_parser(subparser):
     subparser.add_argument(
@@ -43,10 +58,101 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-a', '--all', action='store_true', dest='all',
         help="USE CAREFULLY. Remove ALL installed packages that match each " +
-        "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
-        "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
+             "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
+             "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
     subparser.add_argument(
-        'packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
+        '-d', '--dependents', action='store_true', dest='dependents',
+        help='Also uninstall any packages that depend on the ones given via command line.'
+    )
+    subparser.add_argument(
+        '-y', '--yes-to-all', action='store_true', dest='yes_to_all',
+        help='Assume "yes" is the answer to every confirmation asked to the user.'
+
+    )
+    subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
+
+
+def concretize_specs(specs, allow_multiple_matches=False, force=False):
+    """
+    Returns a list of specs matching the non necessarily concretized specs given from cli
+
+    Args:
+        specs: list of specs to be matched against installed packages
+        allow_multiple_matches : boolean (if True multiple matches for each item in specs are admitted)
+
+    Return:
+        list of specs
+    """
+    specs_from_cli = []  # List of specs that match expressions given via command line
+    has_errors = False
+    for spec in specs:
+        matching = spack.installed_db.query(spec)
+        # For each spec provided, make sure it refers to only one package.
+        # Fail and ask user to be unambiguous if it doesn't
+        if not allow_multiple_matches and len(matching) > 1:
+            tty.error("%s matches multiple packages:" % spec)
+            print()
+            display_specs(matching, long=True, show_flags=True)
+            print()
+            has_errors = True
+
+        # No installed package matches the query
+        if len(matching) == 0 and not force:
+            tty.error("%s does not match any installed packages." % spec)
+            has_errors = True
+
+        specs_from_cli.extend(matching)
+    if has_errors:
+        tty.die(error_message)
+
+    return specs_from_cli
+
+
+def installed_dependents(specs):
+    """
+    Returns a dictionary that maps a spec with a list of its installed dependents
+
+    Args:
+        specs: list of specs to be checked for dependents
+
+    Returns:
+        dictionary of installed dependents
+    """
+    dependents = {}
+    for item in specs:
+        lst = [x for x in item.package.installed_dependents if x not in specs]
+        if lst:
+            lst = list(set(lst))
+            dependents[item] = lst
+    return dependents
+
+
+def do_uninstall(specs, force):
+    """
+    Uninstalls all the specs in a list.
+
+    Args:
+        specs: list of specs to be uninstalled
+        force: force uninstallation (boolean)
+    """
+    packages = []
+    for item in specs:
+        try:
+            # should work if package is known to spack
+            packages.append(item.package)
+        except spack.repository.UnknownPackageError as e:
+            # The package.py file has gone away -- but still
+            # want to uninstall.
+            spack.Package(item).do_uninstall(force=True)
+
+    # Sort packages to be uninstalled by the number of installed dependents
+    # This ensures we do things in the right order
+    def num_installed_deps(pkg):
+        return len(pkg.installed_dependents)
+
+    packages.sort(key=num_installed_deps)
+    for item in packages:
+        item.do_uninstall(force=force)
 
 
 def uninstall(parser, args):
@@ -55,50 +161,34 @@ def uninstall(parser, args):
 
     with spack.installed_db.write_transaction():
         specs = spack.cmd.parse_specs(args.packages)
+        # Gets the list of installed specs that match the ones give via cli
+        uninstall_list = concretize_specs(specs, args.all, args.force)  # takes care of '-a' is given in the cli
+        dependent_list = installed_dependents(uninstall_list)  # takes care of '-d'
 
-        # For each spec provided, make sure it refers to only one package.
-        # Fail and ask user to be unambiguous if it doesn't
-        pkgs = []
-        for spec in specs:
-            matching_specs = spack.installed_db.query(spec)
-            if not args.all and len(matching_specs) > 1:
-                tty.error("%s matches multiple packages:" % spec)
-                print
-                display_specs(matching_specs, long=True)
-                print
-                print "You can either:"
-                print "  a) Use a more specific spec, or"
-                print "  b) use spack uninstall -a to uninstall ALL matching specs."
-                sys.exit(1)
-
-            if len(matching_specs) == 0:
-                if args.force: continue
-                tty.die("%s does not match any installed packages." % spec)
-
-            for s in matching_specs:
-                try:
-                    # should work if package is known to spack
-                    pkgs.append(s.package)
-                except spack.repository.UnknownPackageError, e:
-                    # The package.py file has gone away -- but still
-                    # want to uninstall.
-                    spack.Package(s).do_uninstall(force=True)
-
-        # Sort packages to be uninstalled by the number of installed dependents
-        # This ensures we do things in the right order
-        def num_installed_deps(pkg):
-            return len(pkg.installed_dependents)
-        pkgs.sort(key=num_installed_deps)
-
-        # Uninstall packages in order now.
-        for pkg in pkgs:
-            try:
-                pkg.do_uninstall(force=args.force)
-            except PackageStillNeededError, e:
-                tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
-                print
-                print "The following packages depend on it:"
-                display_specs(e.dependents, long=True)
-                print
-                print "You can use spack uninstall -f to force this action."
-                sys.exit(1)
+        # Process dependent_list and update uninstall_list
+        has_error = False
+        if dependent_list and not args.dependents and not args.force:
+            for spec, lst in dependent_list.items():
+                tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True))
+                print('')
+                print("The following packages depend on it:")
+                display_specs(lst, long=True)
+                print('')
+                has_error = True
+        elif args.dependents:
+            for key, lst in dependent_list.items():
+                uninstall_list.extend(lst)
+            uninstall_list = list(set(uninstall_list))
+
+        if has_error:
+            tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well')
+
+        if not args.yes_to_all:
+            tty.msg("The following packages will be uninstalled : ")
+            print('')
+            display_specs(uninstall_list, long=True, show_flags=True)
+            print('')
+            ask_for_confirmation('Do you want to proceed ? ')
+
+        # Uninstall everything on the list
+        do_uninstall(uninstall_list, args.force)
diff --git a/lib/spack/spack/cmd/unload.py b/lib/spack/spack/cmd/unload.py
index cfb640ee6f..7bd15750ed 100644
--- a/lib/spack/spack/cmd/unload.py
+++ b/lib/spack/spack/cmd/unload.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.modules
diff --git a/lib/spack/spack/cmd/unuse.py b/lib/spack/spack/cmd/unuse.py
index 06176a976b..789a690e9c 100644
--- a/lib/spack/spack/cmd/unuse.py
+++ b/lib/spack/spack/cmd/unuse.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.modules
diff --git a/lib/spack/spack/cmd/url-parse.py b/lib/spack/spack/cmd/url-parse.py
index 077c793d2e..ce12a17d13 100644
--- a/lib/spack/spack/cmd/url-parse.py
+++ b/lib/spack/spack/cmd/url-parse.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 
diff --git a/lib/spack/spack/cmd/urls.py b/lib/spack/spack/cmd/urls.py
index ebab65f7d1..2fe2019a22 100644
--- a/lib/spack/spack/cmd/urls.py
+++ b/lib/spack/spack/cmd/urls.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import spack
diff --git a/lib/spack/spack/cmd/use.py b/lib/spack/spack/cmd/use.py
index c09695cfd3..bbb90fde1b 100644
--- a/lib/spack/spack/cmd/use.py
+++ b/lib/spack/spack/cmd/use.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.modules
diff --git a/lib/spack/spack/cmd/versions.py b/lib/spack/spack/cmd/versions.py
index bba75dae96..ec3a4b2e34 100644
--- a/lib/spack/spack/cmd/versions.py
+++ b/lib/spack/spack/cmd/versions.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 from llnl.util.tty.colify import colify
diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index 8b973d8190..dfae72010a 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re
@@ -92,27 +92,60 @@ class Compiler(object):
     # version suffix for gcc.
     suffixes = [r'-.*']
 
-    # Names of generic arguments used by this compiler
-    arg_rpath   = '-Wl,-rpath,%s'
+    # Default flags used by a compiler to set an rpath
+    @property
+    def cc_rpath_arg(self):
+        return '-Wl,-rpath,'
 
-    # argument used to get C++11 options
-    cxx11_flag = "-std=c++11"
+    @property
+    def cxx_rpath_arg(self):
+        return '-Wl,-rpath,'
 
+#ifdef NEW
+    @property
+    def f77_rpath_arg(self):
+        return '-Wl,-rpath,'
 
+    @property
+    def fc_rpath_arg(self):
+        return '-Wl,-rpath,'
+#else /* not NEW */
     # Cray PrgEnv name that can be used to load this compiler
     PrgEnv = None
 
     # Name of module used to switch versions of this compiler
     PrgEnv_compiler = None
+#endif /* not NEW */
 
+#ifdef NEW
+
+    def __init__(self, cspec, cc, cxx, f77, fc, **kwargs):
+#else /* not NEW */
 
     def __init__(self, cspec, operating_system, paths, modules=[], alias=None):
+#endif /* not NEW */
         def check(exe):
             if exe is None:
                 return None
             _verify_executables(exe)
             return exe
 
+#ifdef NEW
+        self.cc  = check(cc)
+        self.cxx = check(cxx)
+        self.f77 = check(f77)
+        self.fc  = check(fc)
+
+        # Unfortunately have to make sure these params are accepted
+        # in the same order they are returned by sorted(flags)
+        # in compilers/__init__.py
+        self.flags = {}
+        for flag in spack.spec.FlagMap.valid_compiler_flags():
+            value = kwargs.get(flag, None)
+            if value is not None:
+                self.flags[flag] = value.split()
+
+#else /* not NEW */
         self.operating_system = operating_system
 
         self.cc  = check(paths[0])
@@ -124,6 +157,7 @@ class Compiler(object):
             else:
                 self.fc  = check(paths[3])
 
+#endif /* not NEW */
         self.spec = cspec
         self.modules = modules
         self.alias = alias
@@ -132,27 +166,86 @@ class Compiler(object):
     def version(self):
         return self.spec.version
 
+    # This property should be overridden in the compiler subclass if
+    # OpenMP is supported by that compiler
+    @property
+    def openmp_flag(self):
+        # If it is not overridden, assume it is not supported and warn the user
+        tty.die("The compiler you have chosen does not currently support OpenMP.",
+                "If you think it should, please edit the compiler subclass and",
+                "submit a pull request or issue.")
+
+
+    # This property should be overridden in the compiler subclass if
+    # C++11 is supported by that compiler
+    @property
+    def cxx11_flag(self):
+        # If it is not overridden, assume it is not supported and warn the user
+        tty.die("The compiler you have chosen does not currently support C++11.",
+                "If you think it should, please edit the compiler subclass and",
+                "submit a pull request or issue.")
+
+
+    # This property should be overridden in the compiler subclass if
+    # C++14 is supported by that compiler
+    @property
+    def cxx14_flag(self):
+        # If it is not overridden, assume it is not supported and warn the user
+        tty.die("The compiler you have chosen does not currently support C++14.",
+                "If you think it should, please edit the compiler subclass and",
+                "submit a pull request or issue.")
+
+
+
+    #
+    # Compiler classes have methods for querying the version of
+    # specific compiler executables.  This is used when discovering compilers.
+    #
+    # Compiler *instances* are just data objects, and can only be
+    # constructed from an actual set of executables.
+    #
+
+    @classmethod
+    def default_version(cls, cc):
+        """Override just this to override all compiler version functions."""
+        return dumpversion(cc)
+
+    @classmethod
+    def cc_version(cls, cc):
+        return cls.default_version(cc)
+
+    @classmethod
+    def cxx_version(cls, cxx):
+        return cls.default_version(cxx)
+
+    @classmethod
+    def f77_version(cls, f77):
+        return cls.default_version(f77)
+
+    @classmethod
+    def fc_version(cls, fc):
+        return cls.default_version(fc)
 
     @classmethod
     def _find_matches_in_path(cls, compiler_names, detect_version, *path):
         """Finds compilers in the paths supplied.
-        
-            Looks for all combinations of ``compiler_names`` with the
-            ``prefixes`` and ``suffixes`` defined for this compiler
-            class.  If any compilers match the compiler_names,
-            prefixes, or suffixes, uses ``detect_version`` to figure
-            out what version the compiler is.
- 
-            This returns a dict with compilers grouped by (prefix,
-            suffix, version) tuples.  This can be further organized by
-            find().
-         """
+
+           Looks for all combinations of ``compiler_names`` with the
+           ``prefixes`` and ``suffixes`` defined for this compiler
+           class.  If any compilers match the compiler_names,
+           prefixes, or suffixes, uses ``detect_version`` to figure
+           out what version the compiler is.
+
+           This returns a dict with compilers grouped by (prefix,
+           suffix, version) tuples.  This can be further organized by
+           find().
+        """
         if not path:
             path = get_path('PATH')
- 
+
         prefixes = [''] + cls.prefixes
         suffixes = [''] + cls.suffixes
- 
+
         checks = []
         for directory in path:
             if not (os.path.isdir(directory) and
@@ -188,16 +281,12 @@ class Compiler(object):
                 return None
 
         successful = [key for key in parmap(check, checks) if key is not None]
+        # The 'successful' list is ordered like the input paths.
+        # Reverse it here so that the dict creation (last insert wins)
+        # does not spoil the intented precedence.
+        successful.reverse()
         return dict(((v, p, s), path) for v, p, s, path in successful)
 
-    #
-    # Compiler classes have methods for querying the version of
-    # specific compiler executables.  This is used when discovering compilers.
-    #
-    # Compiler *instances* are just data objects, and can only be
-    # constructed from an actual set of executables.
-    #
-
     @classmethod
     def default_version(cls, cc):
         """Override just this to override all compiler version functions."""
@@ -226,7 +315,7 @@ class Compiler(object):
 
 
     def __str__(self):
-        """Return a string represntation of the compiler toolchain."""
+        """Return a string representation of the compiler toolchain."""
         return "%s(%s)" % (
             self.name, '\n     '.join((str(s) for s in (self.cc, self.cxx, self.f77, self.fc, self.modules, str(self.operating_system)))))
 
diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py
index 8ef6e976ba..000ef2058e 100644
--- a/lib/spack/spack/compilers/__init__.py
+++ b/lib/spack/spack/compilers/__init__.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """This module contains functions related to finding compilers on the
 system and configuring Spack to use multiple compilers.
@@ -53,7 +53,6 @@ _imported_compilers_module = 'spack.compilers'
 _path_instance_vars = ['cc', 'cxx', 'f77', 'fc']
 _other_instance_vars = ['modules', 'operating_system']
 
-_default_order = []
 # TODO: customize order in config file
 if platform.system() == 'Darwin':
     _default_order = ['clang', 'gcc', 'intel']
@@ -257,7 +256,15 @@ def compilers_for_spec(compiler_spec, scope=None):
 
             compilers.append(cls(cspec, operating_system, compiler_paths, mods, alias))
 
+#ifdef NEW
+        flags = {}
+        for f in spack.spec.FlagMap.valid_compiler_flags():
+            if f in items:
+                flags[f] = items[f]
+        return cls(cspec, *compiler_paths, **flags)
+#else /* not NEW */
         return compilers
+#endif /* not NEW */
 
     matches = set(find(compiler_spec, scope))
     compilers = []
diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py
index 8226f62eb2..00b406d820 100644
--- a/lib/spack/spack/compilers/clang.py
+++ b/lib/spack/spack/compilers/clang.py
@@ -1,31 +1,33 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
 import spack.compiler as cpr
 from spack.compiler import *
 from spack.util.executable import *
+import llnl.util.tty as tty
+from spack.version import ver
 
 class Clang(Compiler):
     # Subclasses use possible names of C compiler
@@ -47,6 +49,29 @@ class Clang(Compiler):
                    'f77' : 'f77',
                    'fc'  : 'f90' }
 
+    @property
+    def is_apple(self):
+        ver_string = str(self.version)
+        return ver_string.endswith('-apple')
+
+    @property
+    def openmp_flag(self):
+        if self.is_apple:
+            tty.die("Clang from Apple does not support Openmp yet.")
+        else:
+            return "-fopenmp"
+
+    @property
+    def cxx11_flag(self):
+        if self.is_apple:
+            # FIXME: figure out from which version Apple's clang supports c++11
+            return "-std=c++11"
+        else:
+            if self.version < ver('3.3'):
+                tty.die("Only Clang 3.3 and above support c++11.")
+            else:
+                return "-std=c++11"
+
     @classmethod
     def default_version(cls, comp):
         """The '--version' option works for clang compilers.
diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py
index c1fe7496c7..3f552eaece 100644
--- a/lib/spack/spack/compilers/gcc.py
+++ b/lib/spack/spack/compilers/gcc.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import llnl.util.tty as tty
 from spack.compiler import *
@@ -40,7 +40,8 @@ class Gcc(Compiler):
     fc_names = ['gfortran']
 
     # MacPorts builds gcc versions with prefixes and -mp-X.Y suffixes.
-    suffixes = [r'-mp-\d\.\d']
+    # Homebrew and Linuxes may build gcc with -X, -X.Y suffixes
+    suffixes = [r'-mp-\d\.\d', r'-\d\.\d', r'-\d']
 
     # Named wrapper links within spack.build_env_path
     link_paths = {'cc'  : 'gcc/gcc',
@@ -52,13 +53,24 @@ class Gcc(Compiler):
     PrgEnv_compiler = 'gcc'
 
     @property
+    def openmp_flag(self):
+        return "-fopenmp"
+
+    @property
     def cxx11_flag(self):
         if self.version < ver('4.3'):
             tty.die("Only gcc 4.3 and above support c++11.")
         elif self.version < ver('4.7'):
-            return "-std=gnu++0x"
+            return "-std=c++0x"
+        else:
+            return "-std=c++11"
+
+    @property
+    def cxx14_flag(self):
+        if self.version < ver('4.8'):
+            tty.die("Only gcc 4.8 and above support c++14.")
         else:
-            return "-std=gnu++11"
+            return "-std=c++14"
 
     @classmethod
     def fc_version(cls, fc):
diff --git a/lib/spack/spack/compilers/intel.py b/lib/spack/spack/compilers/intel.py
index 80de0867fc..6cad03ff47 100644
--- a/lib/spack/spack/compilers/intel.py
+++ b/lib/spack/spack/compilers/intel.py
@@ -1,28 +1,30 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack.compiler import *
+import llnl.util.tty as tty
+from spack.version import ver
 
 class Intel(Compiler):
     # Subclasses use possible names of C compiler
@@ -47,6 +49,13 @@ class Intel(Compiler):
     PrgEnv_compiler = 'intel'
 
     @property
+    def openmp_flag(self):
+        if self.version < ver('16.0'):
+            return "-openmp"
+        else:
+            return "-qopenmp"
+
+    @property
     def cxx11_flag(self):
         if self.version < ver('11.1'):
             tty.die("Only intel 11.1 and above support c++11.")
@@ -71,5 +80,3 @@ class Intel(Compiler):
         """
         return get_compiler_version(
             comp, '--version', r'\((?:IFORT|ICC)\) ([^ ]+)')
-
-
diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py
index 527a05a090..cee11bc97a 100644
--- a/lib/spack/spack/compilers/nag.py
+++ b/lib/spack/spack/compilers/nag.py
@@ -1,4 +1,29 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 from spack.compiler import *
+import llnl.util.tty as tty
 
 class Nag(Compiler):
     # Subclasses use possible names of C compiler
@@ -20,6 +45,27 @@ class Nag(Compiler):
                    'f77' : 'nag/nagfor',
                    'fc'  : 'nag/nagfor' }
 
+    @property
+    def openmp_flag(self):
+        return "-openmp"
+
+    @property
+    def cxx11_flag(self):
+        # NAG does not have a C++ compiler
+        # However, it can be mixed with a compiler that does support it
+        return "-std=c++11"
+
+    # Unlike other compilers, the NAG compiler passes options to GCC, which
+    # then passes them to the linker. Therefore, we need to doubly wrap the
+    # options with '-Wl,-Wl,,'
+    @property
+    def f77_rpath_arg(self):
+        return '-Wl,-Wl,,-rpath,'
+
+    @property
+    def fc_rpath_arg(self):
+        return '-Wl,-Wl,,-rpath,'
+
     @classmethod
     def default_version(self, comp):
         """The '-V' option works for nag compilers.
diff --git a/lib/spack/spack/compilers/pgi.py b/lib/spack/spack/compilers/pgi.py
index 9c155c1ec4..d3fad15b0c 100644
--- a/lib/spack/spack/compilers/pgi.py
+++ b/lib/spack/spack/compilers/pgi.py
@@ -1,28 +1,29 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack.compiler import *
+import llnl.util.tty as tty
 
 class Pgi(Compiler):
     # Subclasses use possible names of C compiler
@@ -43,9 +44,21 @@ class Pgi(Compiler):
                    'f77' : 'pgi/pgfortran',
                    'fc'  : 'pgi/pgfortran' }
 
+#ifdef NEW
+    @property
+    def openmp_flag(self):
+        return "-mp"
+
+    @property
+    def cxx11_flag(self):
+        return "-std=c++11"
+
+
+#else /* not NEW */
     PrgEnv = 'PrgEnv-pgi'
     PrgEnv_compiler = 'pgi'
 
+#endif /* not NEW */
     @classmethod
     def default_version(cls, comp):
         """The '-V' option works for all the PGI compilers.
@@ -57,4 +70,3 @@ class Pgi(Compiler):
         """
         return get_compiler_version(
             comp, '-V', r'pg[^ ]* ([^ ]+) \d\d\d?-bit target')
-
diff --git a/lib/spack/spack/compilers/xl.py b/lib/spack/spack/compilers/xl.py
index 3041da9047..b1431436ad 100644
--- a/lib/spack/spack/compilers/xl.py
+++ b/lib/spack/spack/compilers/xl.py
@@ -1,29 +1,30 @@
-# -*- coding: utf-8 -*-
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by François Bissey, francois.bissey@canterbury.ac.nz, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack.compiler import *
+import llnl.util.tty as tty
+from spack.version import ver
 
 class Xl(Compiler):
     # Subclasses use possible names of C compiler
@@ -45,6 +46,10 @@ class Xl(Compiler):
                    'fc'  : 'xl/xlf90' }
 
     @property
+    def openmp_flag(self):
+        return "-qsmp=omp"
+
+    @property
     def cxx11_flag(self):
         if self.version < ver('13.1'):
             tty.die("Only xlC 13.1 and above have some c++11 support.")
diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 9ad5271542..72b184dd8f 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 Functions here are used to take abstract specs and make them concrete.
@@ -33,20 +33,18 @@ or user preferences.
 TODO: make this customizable and allow users to configure
       concretization  policies.
 """
-import collections
-from llnl.util.filesystem import join_path
 import spack
 import spack.spec
 import spack.compilers
 import spack.architecture
 import spack.error
-from spack.util.naming import mod_to_class
 from spack.version import *
 from functools import partial
 from spec import DependencyMap
 from itertools import chain
 from spack.config import *
 
+
 class DefaultConcretizer(object):
     """This class doesn't have any state, it just provides some methods for
        concretization.  You can subclass it to override just some of the
@@ -54,10 +52,10 @@ class DefaultConcretizer(object):
     """
 
     def _valid_virtuals_and_externals(self, spec):
-        """Returns a list of spec/external-path pairs for both virtuals and externals
-           that can concretize this spec."""
-        # Get a list of candidate packages that could satisfy this spec
-        packages = []
+        """Returns a list of candidate virtual dep providers and external
+           packages that coiuld be used to concretize a spec."""
+        # First construct a list of concrete candidates to replace spec with.
+        candidates = [spec]
         if spec.virtual:
             providers = spack.repo.providers_for(spec)
             if not providers:
@@ -67,106 +65,72 @@ class DefaultConcretizer(object):
             if not spec_w_preferred_providers:
                 spec_w_preferred_providers = spec
             provider_cmp = partial(spack.pkgsort.provider_compare, spec_w_preferred_providers.name, spec.name)
-            packages = sorted(providers, cmp=provider_cmp)
-        else:
-            packages = [spec]
-
-        # For each candidate package, if it has externals add those to the candidates
-        # if it's a nobuild, then only add the externals.
-        result = []
-        all_compilers = spack.compilers.all_compilers()
-        for pkg in packages:
-            externals = spec_externals(pkg)
-            buildable = not is_spec_nobuild(pkg)
-            if buildable:
-                result.append((pkg, None, None))
+            candidates = sorted(providers, cmp=provider_cmp)
+
+        # For each candidate package, if it has externals, add those to the usable list.
+        # if it's not buildable, then *only* add the externals.
+        usable = []
+        for cspec in candidates:
+            if is_spec_buildable(cspec):
+                usable.append(cspec)
+            externals = spec_externals(cspec)
             for ext in externals:
-                if ext[0].satisfies(spec):
-                    result.append(ext)
-#            if externals:
-#                sorted_externals = sorted(externals, cmp=lambda a,b: a[0].__cmp__(b[0]))
-#                for external in sorted_externals:
-#                    if external[0].satisfies(spec):
-#                        result.append(external)
-        if not result:
+                if ext.satisfies(spec):
+                    usable.append(ext)
+
+        # If nothing is in the usable list now, it's because we aren't
+        # allowed to build anything.
+        if not usable:
             raise NoBuildError(spec)
 
         def cmp_externals(a, b):
-            result = cmp_specs(a[0], b[0])
+            if a.name != b.name:
+                # We're choosing between different providers, so
+                # maintain order from provider sort
+                return candidates.index(a) - candidates.index(b)
+
+            result = cmp_specs(a, b)
             if result != 0:
                 return result
-            if not a[1] and b[1]:
-                return 1
-            if not b[1] and a[1]:
-                return -1
-            return cmp_specs(a[1], b[1])
 
-        result = sorted(result, cmp=cmp_externals)
-        return result
+            # prefer external packages to internal packages.
+            if a.external is None or b.external is None:
+                return -cmp(a.external, b.external)
+            else:
+                return cmp(a.external, b.external)
+
+        usable.sort(cmp=cmp_externals)
+        return usable
 
 
-    def concretize_virtual_and_external(self, spec):
-        """From a list of candidate virtual and external packages, concretize to one that
-           is ABI compatible with the rest of the DAG."""
+    def choose_virtual_or_external(self, spec):
+        """Given a list of candidate virtual and external packages, try to
+           find one that is most ABI compatible.
+        """
         candidates = self._valid_virtuals_and_externals(spec)
         if not candidates:
-            return False
+            return candidates
 
-        # Find the nearest spec in the dag that has a compiler.  We'll use that
-        # spec to test compiler compatibility.
-        other_spec = find_spec(spec, lambda(x): x.compiler)
-        if not other_spec:
-            other_spec = spec.root
+        # Find the nearest spec in the dag that has a compiler.  We'll
+        # use that spec to calibrate compiler compatibility.
+        abi_exemplar = find_spec(spec, lambda(x): x.compiler)
+        if not abi_exemplar:
+            abi_exemplar = spec.root
 
-        # Choose an ABI-compatible candidate, or the first match otherwise.
-        candidate = None
-        if other_spec:
-            candidate = next((c for c in candidates if spack.abi.compatible(c[0], other_spec)), None)
-            if not candidate:
-                # Try a looser ABI matching
-                candidate = next((c for c in candidates if spack.abi.compatible(c[0], other_spec, loose=True)), None)
-        if not candidate:
-            # No ABI matches. Pick the top choice based on the orignal preferences.
-            candidate = candidates[0]
-
-        external_module = candidate[2]
-        external = candidate[1]
-        candidate_spec = candidate[0]
-        changed = False
+        # Make a list including ABI compatibility of specs with the exemplar.
+        strict = [spack.abi.compatible(c, abi_exemplar) for c in candidates]
+        loose  = [spack.abi.compatible(c, abi_exemplar, loose=True) for c in candidates]
+        keys = zip(strict, loose, candidates)
 
-        # If we're external then trim the dependencies
-        if external:
-            if (spec.dependencies):
-                changed = True
-            spec.dependencies = DependencyMap()
-            candidate_spec.dependencies = DependencyMap()
-
-        def fequal(candidate_field, spec_field):
-            return (not candidate_field) or (candidate_field == spec_field)
-        if (fequal(candidate_spec.name, spec.name) and
-            fequal(candidate_spec.versions, spec.versions) and
-            fequal(candidate_spec.compiler, spec.compiler) and
-            fequal(candidate_spec.architecture, spec.architecture) and
-            fequal(candidate_spec.dependencies, spec.dependencies) and
-            fequal(candidate_spec.variants, spec.variants) and
-            fequal(external, spec.external)):
-            return changed
-
-        # Refine this spec to the candidate.
-        if spec.virtual:
-            spec._replace_with(candidate_spec)
-            changed = True
-        if spec._dup(candidate_spec, deps=False, cleardeps=False):
-            changed = True
-
-        if not spec.external and external:
-            spec.external = external
-            changed = True
-        if not spec.external_module and external_module:
-            spec.external_module = external_module
-            changed = True
+        # Sort candidates from most to least compatibility.
+        # Note:
+        #   1. We reverse because True > False.
+        #   2. Sort is stable, so c's keep their order.
+        keys.sort(key=lambda k:k[:2], reverse=True)
 
-        return changed
+        # Pull the candidates back out and return them in order
+        candidates = [c for s,l,c in keys]
+        return candidates
 
 
     def concretize_version(self, spec):
@@ -189,13 +153,17 @@ class DefaultConcretizer(object):
 
         # If there are known available versions, return the most recent
         # version that satisfies the spec
-        pkg = spec.package # Gives error here with dynist
+        pkg = spec.package
         cmp_versions = partial(spack.pkgsort.version_compare, spec.name)
         valid_versions = sorted(
             [v for v in pkg.versions
              if any(v.satisfies(sv) for sv in spec.versions)],
             cmp=cmp_versions)
 
+        def prefer_key(v):
+            return pkg.versions.get(Version(v)).get('preferred', False)
+        valid_versions.sort(key=prefer_key, reverse=True)
+
         if valid_versions:
             spec.versions = ver([valid_versions[0]])
         else:
@@ -272,7 +240,7 @@ class DefaultConcretizer(object):
            the default variants from the package specification.
         """
         changed = False
-        for name, variant in spec.package.variants.items():
+        for name, variant in spec.package_class.variants.items():
             if name not in spec.variants:
                 spec.variants[name] = spack.spec.VariantSpec(name, variant.default)
                 changed = True
@@ -314,7 +282,11 @@ class DefaultConcretizer(object):
             return False
 
         #Find the another spec that has a compiler, or the root if none do
+#ifdef NEW
+        other_spec = spec if spec.compiler else find_spec(spec, lambda(x) : x.compiler)
+#else /* not NEW */
         other_spec = find_spec(spec, lambda(x) : x.compiler)
+#endif /* not NEW */
         if not other_spec:
             other_spec = spec.root
         other_compiler = other_spec.compiler
@@ -343,6 +315,59 @@ class DefaultConcretizer(object):
         return True  # things changed.
 
 
+    def concretize_compiler_flags(self, spec):
+        """
+        The compiler flags are updated to match those of the spec whose
+        compiler is used, defaulting to no compiler flags in the spec.
+        Default specs set at the compiler level will still be added later.
+        """
+        ret = False
+        for flag in spack.spec.FlagMap.valid_compiler_flags():
+            try:
+                nearest = next(p for p in spec.traverse(direction='parents')
+                               if ((p.compiler == spec.compiler and p is not spec)
+                               and flag in p.compiler_flags))
+                if ((not flag in spec.compiler_flags) or
+                    sorted(spec.compiler_flags[flag]) != sorted(nearest.compiler_flags[flag])):
+                    if flag in spec.compiler_flags:
+                        spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) |
+                                                         set(nearest.compiler_flags[flag]))
+                    else:
+                        spec.compiler_flags[flag] = nearest.compiler_flags[flag]
+                    ret = True
+
+            except StopIteration:
+                if (flag in spec.root.compiler_flags and ((not flag in spec.compiler_flags) or
+                    sorted(spec.compiler_flags[flag]) != sorted(spec.root.compiler_flags[flag]))):
+                    if flag in spec.compiler_flags:
+                        spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) |
+                                                         set(spec.root.compiler_flags[flag]))
+                    else:
+                        spec.compiler_flags[flag] = spec.root.compiler_flags[flag]
+                    ret = True
+                else:
+                    if not flag in spec.compiler_flags:
+                        spec.compiler_flags[flag] = []
+
+        # Include the compiler flag defaults from the config files
+        # This ensures that spack will detect conflicts that stem from a change
+        # in default compiler flags.
+        compiler = spack.compilers.compiler_for_spec(spec.compiler)
+        for flag in compiler.flags:
+            if flag not in spec.compiler_flags:
+                spec.compiler_flags[flag] = compiler.flags[flag]
+                if compiler.flags[flag] != []:
+                    ret = True
+            else:
+                if ((sorted(spec.compiler_flags[flag]) != sorted(compiler.flags[flag])) and
+                    (not set(spec.compiler_flags[flag]) >= set(compiler.flags[flag]))):
+                    ret = True
+                    spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) |
+                                                     set(compiler.flags[flag]))
+
+        return ret
+
+
 def find_spec(spec, condition):
     """Searches the dag from spec in an intelligent order and looks
        for a spec that matches a condition"""
@@ -366,7 +391,7 @@ def find_spec(spec, condition):
     if condition(spec):
         return spec
 
-    return None   # Nohting matched the condition.
+    return None   # Nothing matched the condition.
 
 
 def cmp_specs(lhs, rhs):
@@ -404,7 +429,6 @@ def cmp_specs(lhs, rhs):
     return 0
 
 
-
 class UnavailableCompilerVersionError(spack.error.SpackError):
     """Raised when there is no available compiler that satisfies a
        compiler spec."""
@@ -423,8 +447,8 @@ class NoValidVersionError(spack.error.SpackError):
 
 
 class NoBuildError(spack.error.SpackError):
-    """Raised when a package is configured with the nobuild option, but
+    """Raised when a package is configured with the buildable option False, but
        no satisfactory external versions can be found"""
     def __init__(self, spec):
         super(NoBuildError, self).__init__(
-            "The spec '%s' is configured as nobuild, and no matching external installs were found" % spec.name)
+            "The spec '%s' is configured as not buildable, and no matching external installs were found" % spec.name)
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 49f2b90bfc..3d6c175c7c 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -1,26 +1,27 @@
+# flake8: noqa
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """This module implements Spack's configuration file handling.
 
@@ -117,22 +118,20 @@ Will make Spack take compilers *only* from the user configuration, and
 the site configuration will be ignored.
 
 """
+import copy
 import os
 import re
 import sys
-import copy
-import jsonschema
-from jsonschema import Draft4Validator, validators
-import yaml
-from yaml.error import MarkedYAMLError
-from ordereddict_backport import OrderedDict
 
+import jsonschema
 import llnl.util.tty as tty
-from llnl.util.filesystem import mkdirp
-import copy
-
 import spack
+import yaml
+from jsonschema import Draft4Validator, validators
+from llnl.util.filesystem import mkdirp
+from ordereddict_backport import OrderedDict
 from spack.error import SpackError
+from yaml.error import MarkedYAMLError
 
 # Hacked yaml for configuration files preserves line numbers.
 import spack.util.spack_yaml as syaml
@@ -146,7 +145,7 @@ section_schemas = {
         'type': 'object',
         'additionalProperties': False,
         'patternProperties': {
-            'compilers:?': { # optional colon for overriding site config.
+            'compilers:?': {  # optional colon for overriding site config.
                 'type': 'object',
                 'default': {},
                 'additionalProperties': False,
@@ -230,16 +229,20 @@ section_schemas = {
                                 'items' : { 'anyOf' : [ { 'type' : 'string' },
                                                         { 'type' : 'number'}]}}, #version strings
                             'compiler': {
-                                'typee' : 'array',
+                                'type' : 'array',
                                 'default' : [],
                                 'items' : { 'type' : 'string' } }, #compiler specs
-                            'nobuild': {
+                            'buildable': {
                                 'type':  'boolean',
+#ifdef NEW
+                                'default': True,
+#else /* not NEW */
                                 'default': False,
                              },
                             'module': {
                                 'anyOf' : [{'type': 'string'},
                                            {'type': 'null'}]
+#endif /* not NEW */
                              },
                             'providers': {
                                 'type':  'object',
@@ -254,7 +257,125 @@ section_schemas = {
                                 'type' : 'object',
                                 'default' : {},
                             }
-                        },},},},},}
+                        },},},},},},
+
+    'modules': {
+        '$schema': 'http://json-schema.org/schema#',
+        'title': 'Spack module file configuration file schema',
+        'type': 'object',
+        'additionalProperties': False,
+        'definitions': {
+            'array_of_strings': {
+                'type': 'array',
+                'default': [],
+                'items': {
+                    'type': 'string'
+                }
+            },
+            'dictionary_of_strings': {
+                'type': 'object',
+                'patternProperties': {
+                    r'\w[\w-]*': {  # key
+                        'type': 'string'
+                    }
+                }
+            },
+            'dependency_selection': {
+                'type': 'string',
+                'enum': ['none', 'direct', 'all']
+            },
+            'module_file_configuration': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'filter': {
+                        'type': 'object',
+                        'default': {},
+                        'additionalProperties': False,
+                        'properties': {
+                            'environment_blacklist': {
+                                'type': 'array',
+                                'default': [],
+                                'items': {
+                                    'type': 'string'
+                                }
+                            }
+                        }
+                    },
+                    'autoload': {'$ref': '#/definitions/dependency_selection'},
+                    'prerequisites': {'$ref': '#/definitions/dependency_selection'},
+                    'conflict': {'$ref': '#/definitions/array_of_strings'},
+                    'environment': {
+                        'type': 'object',
+                        'default': {},
+                        'additionalProperties': False,
+                        'properties': {
+                            'set': {'$ref': '#/definitions/dictionary_of_strings'},
+                            'unset': {'$ref': '#/definitions/array_of_strings'},
+                            'prepend_path': {'$ref': '#/definitions/dictionary_of_strings'},
+                            'append_path': {'$ref': '#/definitions/dictionary_of_strings'}
+                        }
+                    }
+                }
+            },
+            'module_type_configuration': {
+                'type': 'object',
+                'default': {},
+                'anyOf': [
+                    {
+                        'properties': {
+                            'whitelist': {'$ref': '#/definitions/array_of_strings'},
+                            'blacklist': {'$ref': '#/definitions/array_of_strings'},
+                            'naming_scheme': {
+                                'type': 'string'  # Can we be more specific here?
+                            }
+                        }
+                    },
+                    {
+                        'patternProperties': {r'\w[\w-]*': {'$ref': '#/definitions/module_file_configuration'}}
+                    }
+                ]
+            }
+        },
+        'patternProperties': {
+            r'modules:?': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'prefix_inspections': {
+                        'type': 'object',
+                        'patternProperties': {
+                            r'\w[\w-]*': {  # path to be inspected for existence (relative to prefix)
+                                '$ref': '#/definitions/array_of_strings'
+                            }
+                        }
+                    },
+                    'enable': {
+                        'type': 'array',
+                        'default': [],
+                        'items': {
+                            'type': 'string',
+                            'enum': ['tcl', 'dotkit']
+                        }
+                    },
+                    'tcl': {
+                        'allOf': [
+                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
+                            {}  # Specific tcl extensions
+                        ]
+                    },
+                    'dotkit': {
+                        'allOf': [
+                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
+                            {}  # Specific dotkit extensions
+                        ]
+                    },
+                }
+            },
+        },
+    },
 }
 
 """OrderedDict of config scopes keyed by name.
@@ -264,10 +385,10 @@ config_scopes = OrderedDict()
 
 
 def validate_section_name(section):
-    """Raise a ValueError if the section is not a valid section."""
+    """Exit if the section is not a valid section."""
     if section not in section_schemas:
-        raise ValueError("Invalid config section: '%s'.  Options are %s"
-                         % (section, section_schemas))
+        tty.die("Invalid config section: '%s'. Options are: %s"
+                % (section, " ".join(section_schemas.keys())))
 
 
 def extend_with_default(validator_class):
@@ -301,13 +422,14 @@ def extend_with_default(validator_class):
             yield err
 
     return validators.extend(validator_class, {
-        "properties" : set_defaults,
-        "patternProperties" : set_pp_defaults
+        "properties": set_defaults,
+        "patternProperties": set_pp_defaults
     })
 
 
 DefaultSettingValidator = extend_with_default(Draft4Validator)
 
+
 def validate_section(data, schema):
     """Validate data read in from a Spack YAML file.
 
@@ -342,16 +464,14 @@ class ConfigScope(object):
         validate_section_name(section)
         return os.path.join(self.path, "%s.yaml" % section)
 
-
     def get_section(self, section):
-        if not section in self.sections:
+        if section not in self.sections:
             path   = self.get_section_filename(section)
             schema = section_schemas[section]
             data   = _read_config_file(path, schema)
             self.sections[section] = data
         return self.sections[section]
 
-
     def write_section(self, section):
         filename = self.get_section_filename(section)
         data = self.get_section(section)
@@ -365,7 +485,6 @@ class ConfigScope(object):
         except (yaml.YAMLError, IOError) as e:
             raise ConfigFileError("Error writing to config file: '%s'" % str(e))
 
-
     def clear(self):
         """Empty cached config information."""
         self.sections = {}
@@ -408,7 +527,7 @@ def _read_config_file(filename, schema):
 
     elif not os.path.isfile(filename):
         raise ConfigFileError(
-            "Invlaid configuration. %s exists but is not a file." % filename)
+            "Invalid configuration. %s exists but is not a file." % filename)
 
     elif not os.access(filename, os.R_OK):
         raise ConfigFileError("Config file is not readable: %s" % filename)
@@ -422,11 +541,11 @@ def _read_config_file(filename, schema):
             validate_section(data, schema)
         return data
 
-    except MarkedYAMLError, e:
+    except MarkedYAMLError as e:
         raise ConfigFileError(
             "Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
 
-    except IOError, e:
+    except IOError as e:
         raise ConfigFileError(
             "Error reading configuration file %s: %s" % (filename, str(e)))
 
@@ -471,7 +590,7 @@ def _merge_yaml(dest, source):
     # Source dict is merged into dest.
     elif they_are(dict):
         for sk, sv in source.iteritems():
-            if not sk in dest:
+            if sk not in dest:
                 dest[sk] = copy.copy(sv)
             else:
                 dest[sk] = _merge_yaml(dest[sk], source[sk])
@@ -534,14 +653,19 @@ def update_config(section, update_data, scope=None):
        other yaml-ish structure.
 
     """
+    validate_section_name(section)  # validate section name
+    scope = validate_scope(scope)  # get ConfigScope object from string.
+
     # read in the config to ensure we've got current data
-    get_config(section)
+    configuration = get_config(section)
 
-    validate_section_name(section)       # validate section name
-    scope = validate_scope(scope)   # get ConfigScope object from string.
+    if isinstance(update_data, list):
+        configuration = update_data
+    else:
+        configuration.update(update_data)
 
     # read only the requested section's data.
-    scope.sections[section] = { section : update_data }
+    scope.sections[section] = {section: configuration}
     scope.write_section(section)
 
 
@@ -556,19 +680,27 @@ def print_section(section):
 
 
 def spec_externals(spec):
-    """Return a list of spec, directory pairs for each external location for spec"""
+    """Return a list of external specs (with external directory path filled in),
+       one for each known external installation."""
     allpkgs = get_config('packages')
     name = spec.name
-    spec_locations = []
 
+    external_specs = []
     pkg_paths = allpkgs.get(name, {}).get('paths', None)
     if not pkg_paths:
         return []
 
-    for pkg,path in pkg_paths.iteritems():
-        if not spec.satisfies(pkg):
+    for external_spec, path in pkg_paths.iteritems():
+        if not path:
+            # skip entries without paths (avoid creating extra Specs)
             continue
 
+#ifdef NEW
+        external_spec = spack.spec.Spec(external_spec, external=path)
+        if external_spec.satisfies(spec):
+            external_specs.append(external_spec)
+    return external_specs
+#else /* not NEW */
         module = allpkgs.get(pkg, {}).get('module', None)
         if not path:
             if not module:
@@ -576,21 +708,26 @@ def spec_externals(spec):
             path = get_path_from_module(module)
         spec_locations.append( (spack.spec.Spec(pkg), path, module) )
     return spec_locations
+#endif /* not NEW */
 
 
-def is_spec_nobuild(spec):
-    """Return true if the spec pkgspec is configured as nobuild"""
+def is_spec_buildable(spec):
+    """Return true if the spec pkgspec is configured as buildable"""
     allpkgs = get_config('packages')
-    name = spec.name
-    if not spec.name in allpkgs:
-        return False
-    if not 'nobuild' in allpkgs[spec.name]:
-        return False
-    return allpkgs[spec.name]['nobuild']
+    if spec.name not in allpkgs:
+        return True
+    if 'buildable' not in allpkgs[spec.name]:
+        return True
+    return allpkgs[spec.name]['buildable']
+
+
+class ConfigError(SpackError):
+    pass
 
 
-class ConfigError(SpackError): pass
-class ConfigFileError(ConfigError): pass
+class ConfigFileError(ConfigError):
+    pass
+
 
 def get_path(path, data):
     if path:
@@ -598,6 +735,7 @@ def get_path(path, data):
     else:
         return data
 
+
 class ConfigFormatError(ConfigError):
     """Raised when a configuration format does not match its schema."""
     def __init__(self, validation_error, data):
@@ -632,5 +770,6 @@ class ConfigFormatError(ConfigError):
         message = '%s: %s' % (location, validation_error.message)
         super(ConfigError, self).__init__(message)
 
+
 class ConfigSanityError(ConfigFormatError):
     """Same as ConfigFormatError, raised when config is written by Spack."""
diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index 089d29325e..f3967e6b72 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Spack's installation tracking database.
 
@@ -60,7 +60,7 @@ from spack.repository import UnknownPackageError
 _db_dirname = '.spack-db'
 
 # DB version.  This is stuck in the DB file to track changes in format.
-_db_version = Version('0.9')
+_db_version = Version('0.9.1')
 
 # Default timeout for spack database locks is 5 min.
 _db_lock_timeout = 60
@@ -92,22 +92,24 @@ class InstallRecord(object):
     dependents left.
 
     """
-    def __init__(self, spec, path, installed, ref_count=0):
+    def __init__(self, spec, path, installed, ref_count=0, explicit=False):
         self.spec = spec
         self.path = str(path)
         self.installed = bool(installed)
         self.ref_count = ref_count
+        self.explicit = explicit
 
     def to_dict(self):
         return { 'spec'      : self.spec.to_node_dict(),
                  'path'      : self.path,
                  'installed' : self.installed,
-                 'ref_count' : self.ref_count }
+                 'ref_count' : self.ref_count,
+                 'explicit'  : self.explicit }
 
     @classmethod
     def from_dict(cls, spec, dictionary):
         d = dictionary
-        return InstallRecord(spec, d['path'], d['installed'], d['ref_count'])
+        return InstallRecord(spec, d['path'], d['installed'], d['ref_count'], d.get('explicit', False))
 
 
 class Database(object):
@@ -203,6 +205,11 @@ class Database(object):
 
         spec_dict = installs[hash_key]['spec']
 
+        # Install records don't include hash with spec, so we add it in here
+        # to ensure it is read properly.
+        for name in spec_dict:
+            spec_dict[name]['hash'] = hash_key
+
         # Build spec from dict first.
         spec = Spec.from_node_dict(spec_dict)
 
@@ -248,13 +255,18 @@ class Database(object):
         check('installs' in db, "No 'installs' in YAML DB.")
         check('version'  in db, "No 'version' in YAML DB.")
 
+
+        installs = db['installs']
+
         # TODO: better version checking semantics.
         version = Version(db['version'])
-        if version != _db_version:
+        if version > _db_version:
             raise InvalidDatabaseVersionError(_db_version, version)
+        elif version < _db_version:
+            self.reindex(spack.install_layout)
+            installs = dict((k, v.to_dict()) for k, v in self._data.items())
 
         # Iterate through database and check each record.
-        installs = db['installs']
         data = {}
         for hash_key, rec in installs.items():
             try:
@@ -370,7 +382,7 @@ class Database(object):
             self.reindex(spack.install_layout)
 
 
-    def _add(self, spec, path, directory_layout=None):
+    def _add(self, spec, path, directory_layout=None, explicit=False):
         """Add an install record for spec at path to the database.
 
         This assumes that the spec is not already installed. It
@@ -392,7 +404,7 @@ class Database(object):
             rec.path = path
 
         else:
-            self._data[key] = InstallRecord(spec, path, True)
+            self._data[key] = InstallRecord(spec, path, True, explicit=explicit)
             for dep in spec.dependencies.values():
                 self._increment_ref_count(dep, directory_layout)
 
@@ -415,7 +427,7 @@ class Database(object):
         self._data[key].ref_count += 1
 
     @_autospec
-    def add(self, spec, path):
+    def add(self, spec, path, explicit=False):
         """Add spec at path to database, locking and reading DB to sync.
 
         ``add()`` will lock and read from the DB on disk.
@@ -424,7 +436,7 @@ class Database(object):
         # TODO: ensure that spec is concrete?
         # Entire add is transactional.
         with self.write_transaction():
-            self._add(spec, path)
+            self._add(spec, path, explicit=explicit)
 
 
     def _get_matching_spec_key(self, spec, **kwargs):
@@ -513,7 +525,7 @@ class Database(object):
             # TODO: conditional way to do this instead of catching exceptions
 
 
-    def query(self, query_spec=any, known=any, installed=True):
+    def query(self, query_spec=any, known=any, installed=True, explicit=any):
         """Run a query on the database.
 
         ``query_spec``
@@ -553,6 +565,8 @@ class Database(object):
             for key, rec in self._data.items():
                 if installed is not any and rec.installed != installed:
                     continue
+                if explicit is not any and rec.explicit != explicit:
+                    continue
                 if known is not any and spack.repo.exists(rec.spec.name) != known:
                     continue
                 if query_spec is any or rec.spec.satisfies(query_spec):
diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py
index f0691765ba..ca8f21dc08 100644
--- a/lib/spack/spack/directives.py
+++ b/lib/spack/spack/directives.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """This package contains directives that can be used within a package.
 
@@ -45,11 +45,8 @@ The available directives are:
   * ``resource``
 
 """
-__all__ = ['depends_on', 'extends', 'provides', 'patch', 'version',
-           'variant', 'resource']
 
 import re
-import inspect
 import os.path
 import functools
 
@@ -67,6 +64,9 @@ from spack.spec import Spec, parse_anonymous_spec
 from spack.resource import Resource
 from spack.fetch_strategy import from_kwargs
 
+__all__ = ['depends_on', 'extends', 'provides', 'patch', 'version', 'variant',
+           'resource']
+
 #
 # This is a list of all directives, built up as they are defined in
 # this file.
@@ -122,15 +122,14 @@ class directive(object):
 
     def __init__(self, dicts=None):
         if isinstance(dicts, basestring):
-            dicts = (dicts,)
+            dicts = (dicts, )
         elif type(dicts) not in (list, tuple):
             raise TypeError(
-                "dicts arg must be list, tuple, or string. Found %s"
-                % type(dicts))
+                "dicts arg must be list, tuple, or string. Found %s" %
+                type(dicts))
 
         self.dicts = dicts
 
-
     def ensure_dicts(self, pkg):
         """Ensure that a package has the dicts required by this directive."""
         for d in self.dicts:
@@ -142,7 +141,6 @@ class directive(object):
                 raise spack.error.SpackError(
                     "Package %s has non-dict %s attribute!" % (pkg, d))
 
-
     def __call__(self, directive_function):
         directives[directive_function.__name__] = self
 
@@ -263,7 +261,8 @@ def variant(pkg, name, default=False, description=""):
     description = str(description).strip()
 
     if not re.match(spack.spec.identifier_re, name):
-        raise DirectiveError("Invalid variant name in %s: '%s'" % (pkg.name, name))
+        raise DirectiveError("Invalid variant name in %s: '%s'" %
+                             (pkg.name, name))
 
     pkg.variants[name] = Variant(default, description)
 
@@ -271,31 +270,37 @@ def variant(pkg, name, default=False, description=""):
 @directive('resources')
 def resource(pkg, **kwargs):
     """
-    Define an external resource to be fetched and staged when building the package. Based on the keywords present in the
-    dictionary the appropriate FetchStrategy will be used for the resource. Resources are fetched and staged in their
-    own folder inside spack stage area, and then linked into the stage area of the package that needs them.
+    Define an external resource to be fetched and staged when building the
+    package. Based on the keywords present in the dictionary the appropriate
+    FetchStrategy will be used for the resource. Resources are fetched and
+    staged in their own folder inside spack stage area, and then linked into
+    the stage area of the package that needs them.
 
     List of recognized keywords:
 
-    * 'when' : (optional) represents the condition upon which the resource is needed
-    * 'destination' : (optional) path where to link the resource. This path must be relative to the main package stage
-    area.
-    * 'placement' : (optional) gives the possibility to fine tune how the resource is linked into the main package stage
-    area.
+    * 'when' : (optional) represents the condition upon which the resource is
+    needed
+    * 'destination' : (optional) path where to link the resource. This path
+    must be relative to the main package stage area.
+    * 'placement' : (optional) gives the possibility to fine tune how the
+    resource is linked into the main package stage area.
     """
     when = kwargs.get('when', pkg.name)
     destination = kwargs.get('destination', "")
     placement = kwargs.get('placement', None)
     # Check if the path is relative
     if os.path.isabs(destination):
-        message = "The destination keyword of a resource directive can't be an absolute path.\n"
+        message = "The destination keyword of a resource directive can't be"
+        " an absolute path.\n"
         message += "\tdestination : '{dest}\n'".format(dest=destination)
         raise RuntimeError(message)
     # Check if the path falls within the main package stage area
-    test_path = 'stage_folder_root/'
-    normalized_destination = os.path.normpath(join_path(test_path, destination))  # Normalized absolute path
+    test_path = 'stage_folder_root'
+    normalized_destination = os.path.normpath(join_path(test_path, destination)
+                                              )  # Normalized absolute path
     if test_path not in normalized_destination:
-        message = "The destination folder of a resource must fall within the main package stage directory.\n"
+        message = "The destination folder of a resource must fall within the"
+        " main package stage directory.\n"
         message += "\tdestination : '{dest}'\n".format(dest=destination)
         raise RuntimeError(message)
     when_spec = parse_anonymous_spec(when, pkg.name)
@@ -307,6 +312,7 @@ def resource(pkg, **kwargs):
 
 class DirectiveError(spack.error.SpackError):
     """This is raised when something is wrong with a package directive."""
+
     def __init__(self, directive, message):
         super(DirectiveError, self).__init__(message)
         self.directive = directive
@@ -314,6 +320,7 @@ class DirectiveError(spack.error.SpackError):
 
 class CircularReferenceError(DirectiveError):
     """This is raised when something depends on itself."""
+
     def __init__(self, directive, package):
         super(CircularReferenceError, self).__init__(
             directive,
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 96a49554ae..7e20365b0f 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
 import os
@@ -150,7 +150,7 @@ class DirectoryLayout(object):
         if os.path.exists(path):
             try:
                 shutil.rmtree(path)
-            except exceptions.OSError, e:
+            except exceptions.OSError as e:
                 raise RemoveFailedError(spec, path, e)
 
         path = os.path.dirname(path)
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
new file mode 100644
index 0000000000..af642dcc9b
--- /dev/null
+++ b/lib/spack/spack/environment.py
@@ -0,0 +1,306 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import collections
+import inspect
+import os
+import os.path
+
+
+class NameModifier(object):
+    def __init__(self, name, **kwargs):
+        self.name = name
+        self.args = {'name': name}
+        self.args.update(kwargs)
+
+
+class NameValueModifier(object):
+    def __init__(self, name, value, **kwargs):
+        self.name = name
+        self.value = value
+        self.separator = kwargs.get('separator', ':')
+        self.args = {'name': name, 'value': value, 'delim': self.separator}
+        self.args.update(kwargs)
+
+
+class SetEnv(NameValueModifier):
+    def execute(self):
+        os.environ[self.name] = str(self.value)
+
+
+class UnsetEnv(NameModifier):
+    def execute(self):
+        # Avoid throwing if the variable was not set
+        os.environ.pop(self.name, None)
+
+
+class SetPath(NameValueModifier):
+    def execute(self):
+        string_path = concatenate_paths(self.value, separator=self.separator)
+        os.environ[self.name] = string_path
+
+
+class AppendPath(NameValueModifier):
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(
+            self.separator) if environment_value else []
+        directories.append(os.path.normpath(self.value))
+        os.environ[self.name] = self.separator.join(directories)
+
+
+class PrependPath(NameValueModifier):
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(
+            self.separator) if environment_value else []
+        directories = [os.path.normpath(self.value)] + directories
+        os.environ[self.name] = self.separator.join(directories)
+
+
+class RemovePath(NameValueModifier):
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(
+            self.separator) if environment_value else []
+        directories = [os.path.normpath(x) for x in directories
+                       if x != os.path.normpath(self.value)]
+        os.environ[self.name] = self.separator.join(directories)
+
+
+class EnvironmentModifications(object):
+    """
+    Keeps track of requests to modify the current environment.
+
+    Each call to a method to modify the environment stores the extra
+    information on the caller in the request:
+    - 'filename' : filename of the module where the caller is defined
+    - 'lineno': line number where the request occurred
+    - 'context' : line of code that issued the request that failed
+    """
+
+    def __init__(self, other=None):
+        """
+        Initializes a new instance, copying commands from other if not None
+
+        Args:
+            other: another instance of EnvironmentModifications (optional)
+        """
+        self.env_modifications = []
+        if other is not None:
+            self.extend(other)
+
+    def __iter__(self):
+        return iter(self.env_modifications)
+
+    def __len__(self):
+        return len(self.env_modifications)
+
+    def extend(self, other):
+        self._check_other(other)
+        self.env_modifications.extend(other.env_modifications)
+
+    @staticmethod
+    def _check_other(other):
+        if not isinstance(other, EnvironmentModifications):
+            raise TypeError(
+                'other must be an instance of EnvironmentModifications')
+
+    def _get_outside_caller_attributes(self):
+        stack = inspect.stack()
+        try:
+            _, filename, lineno, _, context, index = stack[2]
+            context = context[index].strip()
+        except Exception:
+            filename = 'unknown file'
+            lineno = 'unknown line'
+            context = 'unknown context'
+        args = {'filename': filename, 'lineno': lineno, 'context': context}
+        return args
+
+    def set(self, name, value, **kwargs):
+        """
+        Stores in the current object a request to set an environment variable
+
+        Args:
+            name: name of the environment variable to be set
+            value: value of the environment variable
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = SetEnv(name, value, **kwargs)
+        self.env_modifications.append(item)
+
+    def unset(self, name, **kwargs):
+        """
+        Stores in the current object a request to unset an environment variable
+
+        Args:
+            name: name of the environment variable to be set
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = UnsetEnv(name, **kwargs)
+        self.env_modifications.append(item)
+
+    def set_path(self, name, elts, **kwargs):
+        """
+        Stores a request to set a path generated from a list.
+
+        Args:
+            name: name o the environment variable to be set.
+            elts: elements of the path to set.
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = SetPath(name, elts, **kwargs)
+        self.env_modifications.append(item)
+
+    def append_path(self, name, path, **kwargs):
+        """
+        Stores in the current object a request to append a path to a path list
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be appended
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = AppendPath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def prepend_path(self, name, path, **kwargs):
+        """
+        Same as `append_path`, but the path is pre-pended
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be pre-pended
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = PrependPath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def remove_path(self, name, path, **kwargs):
+        """
+        Stores in the current object a request to remove a path from a path
+        list
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be removed
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = RemovePath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def group_by_name(self):
+        """
+        Returns a dict of the modifications grouped by variable name
+
+        Returns:
+            dict mapping the environment variable name to the modifications to
+            be done on it
+        """
+        modifications = collections.defaultdict(list)
+        for item in self:
+            modifications[item.name].append(item)
+        return modifications
+
+    def clear(self):
+        """
+        Clears the current list of modifications
+        """
+        self.env_modifications.clear()
+
+    def apply_modifications(self):
+        """
+        Applies the modifications and clears the list
+        """
+        modifications = self.group_by_name()
+        # Apply modifications one variable at a time
+        for name, actions in sorted(modifications.items()):
+            for x in actions:
+                x.execute()
+
+
+def concatenate_paths(paths, separator=':'):
+    """
+    Concatenates an iterable of paths into a string of paths separated by
+    separator, defaulting to colon
+
+    Args:
+        paths: iterable of paths
+        separator: the separator to use, default ':'
+
+    Returns:
+        string
+    """
+    return separator.join(str(item) for item in paths)
+
+
+def set_or_unset_not_first(variable, changes, errstream):
+    """
+    Check if we are going to set or unset something after other modifications
+    have already been requested
+    """
+    indexes = [ii for ii, item in enumerate(changes)
+               if ii != 0 and type(item) in [SetEnv, UnsetEnv]]
+    if indexes:
+        good = '\t    \t{context} at {filename}:{lineno}'
+        nogood = '\t--->\t{context} at {filename}:{lineno}'
+        message = 'Suspicious requests to set or unset the variable \'{var}\' found'  # NOQA: ignore=E501
+        errstream(message.format(var=variable))
+        for ii, item in enumerate(changes):
+            print_format = nogood if ii in indexes else good
+            errstream(print_format.format(**item.args))
+
+
+def validate(env, errstream):
+    """
+    Validates the environment modifications to check for the presence of
+    suspicious patterns. Prompts a warning for everything that was found
+
+    Current checks:
+    - set or unset variables after other changes on the same variable
+
+    Args:
+        env: list of environment modifications
+    """
+    modifications = env.group_by_name()
+    for variable, list_of_changes in sorted(modifications.items()):
+        set_or_unset_not_first(variable, list_of_changes, errstream)
+
+
+def filter_environment_blacklist(env, variables):
+    """
+    Generator that filters out any change to environment variables present in
+    the input list
+
+    Args:
+        env: list of environment modifications
+        variables: list of variable names to be filtered
+
+    Yields:
+        items in env if they are not in variables
+    """
+    for item in env:
+        if item.name not in variables:
+            yield item
diff --git a/lib/spack/spack/error.py b/lib/spack/spack/error.py
index 0c2e7eb53c..85ad2fe249 100644
--- a/lib/spack/spack/error.py
+++ b/lib/spack/spack/error.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 0d0a7db8a9..7c8cebe0c9 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 Fetch strategies are used to download source code into a staging area
@@ -57,7 +57,6 @@ from spack.version import Version, ver
 from spack.util.compression import decompressor_for, extension
 
 import spack.util.pattern as pattern
-
 """List of all fetch strategies, created by FetchStrategy metaclass."""
 all_strategies = []
 
@@ -82,13 +81,16 @@ class FetchStrategy(object):
 
     class __metaclass__(type):
         """This metaclass registers all fetch strategies in a list."""
+
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.enabled: all_strategies.append(cls)
+            if cls.enabled:
+                all_strategies.append(cls)
 
     def __init__(self):
-        # The stage is initialized late, so that fetch strategies can be constructed
-        # at package construction time.  This is where things will be fetched.
+        # The stage is initialized late, so that fetch strategies can be
+        # constructed at package construction time.  This is where things
+        # will be fetched.
         self.stage = None
 
     def set_stage(self, stage):
@@ -97,15 +99,20 @@ class FetchStrategy(object):
         self.stage = stage
 
     # Subclasses need to implement these methods
-    def fetch(self):   pass  # Return True on success, False on fail.
+    def fetch(self):
+        pass  # Return True on success, False on fail.
 
-    def check(self):   pass  # Do checksum.
+    def check(self):
+        pass  # Do checksum.
 
-    def expand(self):  pass  # Expand archive.
+    def expand(self):
+        pass  # Expand archive.
 
-    def reset(self):   pass  # Revert to freshly downloaded state.
+    def reset(self):
+        pass  # Revert to freshly downloaded state.
 
-    def archive(self, destination): pass  # Used to create tarball for mirror.
+    def archive(self, destination):
+        pass  # Used to create tarball for mirror.
 
     def __str__(self):  # Should be human readable URL.
         return "FetchStrategy.__str___"
@@ -139,10 +146,12 @@ class URLFetchStrategy(FetchStrategy):
         # If URL or digest are provided in the kwargs, then prefer
         # those values.
         self.url = kwargs.get('url', None)
-        if not self.url: self.url = url
+        if not self.url:
+            self.url = url
 
         self.digest = kwargs.get('md5', None)
-        if not self.digest: self.digest = digest
+        if not self.digest:
+            self.digest = digest
 
         self.expand_archive = kwargs.get('expand', True)
 
@@ -157,12 +166,30 @@ class URLFetchStrategy(FetchStrategy):
             tty.msg("Already downloaded %s" % self.archive_file)
             return
 
+        possible_files = self.stage.expected_archive_files
+        save_file = None
+        partial_file = None
+        if possible_files:
+            save_file = self.stage.expected_archive_files[0]
+            partial_file = self.stage.expected_archive_files[0] + '.part'
+
         tty.msg("Trying to fetch from %s" % self.url)
 
-        curl_args = ['-O',  # save file to disk
-                     '-f',  # fail on >400 errors
-                     '-D', '-',  # print out HTML headers
-                     '-L', self.url, ]
+        if partial_file:
+            save_args = ['-C',
+                         '-',  # continue partial downloads
+                         '-o',
+                         partial_file]  # use a .part file
+        else:
+            save_args = ['-O']
+
+        curl_args = save_args + [
+            '-f',  # fail on >400 errors
+            '-D',
+            '-',  # print out HTML headers
+            '-L',  # resolve 3xx redirects
+            self.url,
+        ]
 
         if sys.stdout.isatty():
             curl_args.append('-#')  # status bar when using a tty
@@ -170,44 +197,52 @@ class URLFetchStrategy(FetchStrategy):
             curl_args.append('-sS')  # just errors when not.
 
         # Run curl but grab the mime type from the http headers
-        headers = spack.curl(
-            *curl_args, output=str, fail_on_error=False)
+        headers = spack.curl(*curl_args, output=str, fail_on_error=False)
 
         if spack.curl.returncode != 0:
             # clean up archive on failure.
             if self.archive_file:
                 os.remove(self.archive_file)
 
+            if partial_file and os.path.exists(partial_file):
+                os.remove(partial_file)
+
             if spack.curl.returncode == 22:
                 # This is a 404.  Curl will print the error.
                 raise FailedDownloadError(
-                        self.url, "URL %s was not found!" % self.url)
+                    self.url, "URL %s was not found!" % self.url)
 
             elif spack.curl.returncode == 60:
                 # This is a certificate error.  Suggest spack -k
                 raise FailedDownloadError(
-                        self.url,
-                        "Curl was unable to fetch due to invalid certificate. "
-                        "This is either an attack, or your cluster's SSL configuration "
-                        "is bad.  If you believe your SSL configuration is bad, you "
-                        "can try running spack -k, which will not check SSL certificates."
-                        "Use this at your own risk.")
+                    self.url,
+                    "Curl was unable to fetch due to invalid certificate. "
+                    "This is either an attack, or your cluster's SSL "
+                    "configuration is bad.  If you believe your SSL "
+                    "configuration is bad, you can try running spack -k, "
+                    "which will not check SSL certificates."
+                    "Use this at your own risk.")
 
             else:
                 # This is some other curl error.  Curl will print the
                 # error, but print a spack message too
                 raise FailedDownloadError(
-                        self.url, "Curl failed with error %d" % spack.curl.returncode)
+                    self.url,
+                    "Curl failed with error %d" % spack.curl.returncode)
 
         # Check if we somehow got an HTML file rather than the archive we
         # asked for.  We only look at the last content type, to handle
         # redirects properly.
         content_types = re.findall(r'Content-Type:[^\r\n]+', headers)
         if content_types and 'text/html' in content_types[-1]:
-            tty.warn("The contents of " + self.archive_file + " look like HTML.",
-                     "The checksum will likely be bad.  If it is, you can use",
-                     "'spack clean <package>' to remove the bad archive, then fix",
-                     "your internet gateway issue and install again.")
+            tty.warn(
+                "The contents of " + self.archive_file + " look like HTML.",
+                "The checksum will likely be bad.  If it is, you can use",
+                "'spack clean <package>' to remove the bad archive, then fix",
+                "your internet gateway issue and install again.")
+
+        if save_file:
+            os.rename(partial_file, save_file)
 
         if not self.archive_file:
             raise FailedDownloadError(self.url)
@@ -227,14 +262,16 @@ class URLFetchStrategy(FetchStrategy):
 
         self.stage.chdir()
         if not self.archive_file:
-            raise NoArchiveFileError("URLFetchStrategy couldn't find archive file",
-                                     "Failed on expand() for URL %s" % self.url)
+            raise NoArchiveFileError(
+                "URLFetchStrategy couldn't find archive file",
+                "Failed on expand() for URL %s" % self.url)
 
         decompress = decompressor_for(self.archive_file)
 
         # Expand all tarballs in their own directory to contain
         # exploding tarballs.
-        tarball_container = os.path.join(self.stage.path, "spack-expanded-archive")
+        tarball_container = os.path.join(self.stage.path,
+                                         "spack-expanded-archive")
         mkdirp(tarball_container)
         os.chdir(tarball_container)
         decompress(self.archive_file)
@@ -275,22 +312,33 @@ class URLFetchStrategy(FetchStrategy):
         """Check the downloaded archive against a checksum digest.
            No-op if this stage checks code out of a repository."""
         if not self.digest:
-            raise NoDigestError("Attempt to check URLFetchStrategy with no digest.")
+            raise NoDigestError(
+                "Attempt to check URLFetchStrategy with no digest.")
 
         checker = crypto.Checker(self.digest)
         if not checker.check(self.archive_file):
             raise ChecksumError(
-                    "%s checksum failed for %s" % (checker.hash_name, self.archive_file),
-                    "Expected %s but got %s" % (self.digest, checker.sum))
+                "%s checksum failed for %s" %
+                (checker.hash_name, self.archive_file),
+                "Expected %s but got %s" % (self.digest, checker.sum))
 
     @_needs_stage
     def reset(self):
-        """Removes the source path if it exists, then re-expands the archive."""
+        """
+        Removes the source path if it exists, then re-expands the archive.
+        """
         if not self.archive_file:
-            raise NoArchiveFileError("Tried to reset URLFetchStrategy before fetching",
-                                     "Failed on reset() for URL %s" % self.url)
-        if self.stage.source_path:
-            shutil.rmtree(self.stage.source_path, ignore_errors=True)
+            raise NoArchiveFileError(
+                "Tried to reset URLFetchStrategy before fetching",
+                "Failed on reset() for URL %s" % self.url)
+
+        # Remove everythigng but the archive from the stage
+        for filename in os.listdir(self.stage.path):
+            abspath = os.path.join(self.stage.path, filename)
+            if abspath != self.archive_file:
+                shutil.rmtree(abspath, ignore_errors=True)
+
+        # Expand the archive again
         self.expand()
 
     def __repr__(self):
@@ -311,14 +359,16 @@ class VCSFetchStrategy(FetchStrategy):
 
         # Set a URL based on the type of fetch strategy.
         self.url = kwargs.get(name, None)
-        if not self.url: raise ValueError(
+        if not self.url:
+            raise ValueError(
                 "%s requires %s argument." % (self.__class__, name))
 
         # Ensure that there's only one of the rev_types
         if sum(k in kwargs for k in rev_types) > 1:
             raise FetchStrategyError(
-                    "Supply only one of %s to fetch with %s" % (
-                        comma_or(rev_types), name))
+                "Supply only one of %s to fetch with %s" % (
+                    comma_or(rev_types), name
+                ))
 
         # Set attributes for each rev type.
         for rt in rev_types:
@@ -356,32 +406,93 @@ class VCSFetchStrategy(FetchStrategy):
         return "%s<%s>" % (self.__class__, self.url)
 
 
+class GoFetchStrategy(VCSFetchStrategy):
+    """
+    Fetch strategy that employs the `go get` infrastructure
+    Use like this in a package:
+
+       version('name',
+               go='github.com/monochromegane/the_platinum_searcher/...')
+
+    Go get does not natively support versions, they can be faked with git
+    """
+    enabled = True
+    required_attributes = ('go', )
+
+    def __init__(self, **kwargs):
+        # Discards the keywords in kwargs that may conflict with the next
+        # call to __init__
+        forwarded_args = copy.copy(kwargs)
+        forwarded_args.pop('name', None)
+
+        super(GoFetchStrategy, self).__init__('go', **forwarded_args)
+        self._go = None
+
+    @property
+    def go_version(self):
+        vstring = self.go('version', output=str).split(' ')[2]
+        return Version(vstring)
+
+    @property
+    def go(self):
+        if not self._go:
+            self._go = which('go', required=True)
+        return self._go
+
+    @_needs_stage
+    def fetch(self):
+        self.stage.chdir()
+
+        tty.msg("Trying to get go resource:", self.url)
+
+        try:
+            os.mkdir('go')
+        except OSError:
+            pass
+        env = dict(os.environ)
+        env['GOPATH'] = os.path.join(os.getcwd(), 'go')
+        self.go('get', '-v', '-d', self.url, env=env)
+
+    def archive(self, destination):
+        super(GoFetchStrategy, self).archive(destination, exclude='.git')
+
+    @_needs_stage
+    def reset(self):
+        self.stage.chdir_to_source()
+        self.go('clean')
+
+    def __str__(self):
+        return "[go] %s" % self.url
+
+
 class GitFetchStrategy(VCSFetchStrategy):
-    """Fetch strategy that gets source code from a git repository.
-       Use like this in a package:
+    """
+    Fetch strategy that gets source code from a git repository.
+    Use like this in a package:
 
-           version('name', git='https://github.com/project/repo.git')
+        version('name', git='https://github.com/project/repo.git')
 
-       Optionally, you can provide a branch, or commit to check out, e.g.:
+    Optionally, you can provide a branch, or commit to check out, e.g.:
 
-           version('1.1', git='https://github.com/project/repo.git', tag='v1.1')
+        version('1.1', git='https://github.com/project/repo.git', tag='v1.1')
 
-       You can use these three optional attributes in addition to ``git``:
+    You can use these three optional attributes in addition to ``git``:
 
-           * ``branch``: Particular branch to build from (default is master)
-           * ``tag``: Particular tag to check out
-           * ``commit``: Particular commit hash in the repo
+        * ``branch``: Particular branch to build from (default is master)
+        * ``tag``: Particular tag to check out
+        * ``commit``: Particular commit hash in the repo
     """
     enabled = True
-    required_attributes = ('git',)
+    required_attributes = ('git', )
 
     def __init__(self, **kwargs):
-        # Discards the keywords in kwargs that may conflict with the next call to __init__
+        # Discards the keywords in kwargs that may conflict with the next call
+        # to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
 
         super(GitFetchStrategy, self).__init__(
-                'git', 'tag', 'branch', 'commit', **forwarded_args)
+            'git', 'tag', 'branch', 'commit', **forwarded_args)
         self._git = None
 
     @property
@@ -489,12 +600,13 @@ class SvnFetchStrategy(VCSFetchStrategy):
     required_attributes = ['svn']
 
     def __init__(self, **kwargs):
-        # Discards the keywords in kwargs that may conflict with the next call to __init__
+        # Discards the keywords in kwargs that may conflict with the next call
+        # to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
 
         super(SvnFetchStrategy, self).__init__(
-                'svn', 'revision', **forwarded_args)
+            'svn', 'revision', **forwarded_args)
         self._svn = None
         if self.revision is not None:
             self.revision = str(self.revision)
@@ -550,32 +662,35 @@ class SvnFetchStrategy(VCSFetchStrategy):
 
 
 class HgFetchStrategy(VCSFetchStrategy):
-    """Fetch strategy that gets source code from a Mercurial repository.
-       Use like this in a package:
+    """
+    Fetch strategy that gets source code from a Mercurial repository.
+    Use like this in a package:
 
-           version('name', hg='https://jay.grs.rwth-aachen.de/hg/lwm2')
+        version('name', hg='https://jay.grs.rwth-aachen.de/hg/lwm2')
 
-       Optionally, you can provide a branch, or revision to check out, e.g.:
+    Optionally, you can provide a branch, or revision to check out, e.g.:
 
-           version('torus', hg='https://jay.grs.rwth-aachen.de/hg/lwm2', branch='torus')
+        version('torus',
+                hg='https://jay.grs.rwth-aachen.de/hg/lwm2', branch='torus')
 
-       You can use the optional 'revision' attribute to check out a
-       branch, tag, or particular revision in hg.  To prevent
-       non-reproducible builds, using a moving target like a branch is
-       discouraged.
+    You can use the optional 'revision' attribute to check out a
+    branch, tag, or particular revision in hg.  To prevent
+    non-reproducible builds, using a moving target like a branch is
+    discouraged.
 
-           * ``revision``: Particular revision, branch, or tag.
+        * ``revision``: Particular revision, branch, or tag.
     """
     enabled = True
     required_attributes = ['hg']
 
     def __init__(self, **kwargs):
-        # Discards the keywords in kwargs that may conflict with the next call to __init__
+        # Discards the keywords in kwargs that may conflict with the next call
+        # to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
 
         super(HgFetchStrategy, self).__init__(
-                'hg', 'revision', **forwarded_args)
+            'hg', 'revision', **forwarded_args)
         self._hg = None
 
     @property
@@ -649,7 +764,8 @@ def from_kwargs(**kwargs):
             return fetcher(**kwargs)
     # Raise an error in case we can't instantiate any known strategy
     message = "Cannot instantiate any FetchStrategy"
-    long_message = message + " from the given arguments : {arguments}".format(srguments=kwargs)
+    long_message = message + " from the given arguments : {arguments}".format(
+        srguments=kwargs)
     raise FetchError(message, long_message)
 
 
@@ -661,7 +777,7 @@ def for_package_version(pkg, version):
     """Determine a fetch strategy based on the arguments supplied to
        version() in the package description."""
     # If it's not a known version, extrapolate one.
-    if not version in pkg.versions:
+    if version not in pkg.versions:
         url = pkg.url_for_version(version)
         if not url:
             raise InvalidArgsError(pkg, version)
@@ -699,7 +815,7 @@ class FailedDownloadError(FetchError):
 
     def __init__(self, url, msg=""):
         super(FailedDownloadError, self).__init__(
-                "Failed to fetch file from URL: %s" % url, msg)
+            "Failed to fetch file from URL: %s" % url, msg)
         self.url = url
 
 
@@ -715,7 +831,8 @@ class NoDigestError(FetchError):
 
 class InvalidArgsError(FetchError):
     def __init__(self, pkg, version):
-        msg = "Could not construct a fetch strategy for package %s at version %s"
+        msg = ("Could not construct a fetch strategy for package %s at "
+               "version %s")
         msg %= (pkg.name, version)
         super(InvalidArgsError, self).__init__(msg)
 
@@ -732,4 +849,5 @@ class NoStageError(FetchError):
 
     def __init__(self, method):
         super(NoStageError, self).__init__(
-                "Must call FetchStrategy.set_stage() before calling %s" % method.__name__)
+            "Must call FetchStrategy.set_stage() before calling %s" %
+            method.__name__)
diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py
index f3732dfbff..22058d41d8 100644
--- a/lib/spack/spack/graph.py
+++ b/lib/spack/spack/graph.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Functions for graphing DAGs of dependencies.
 
diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py
index 2765f7be39..902e488eca 100644
--- a/lib/spack/spack/hooks/__init__.py
+++ b/lib/spack/spack/hooks/__init__.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """This package contains modules with hooks for various stages in the
    Spack install process.  You can add modules here and they'll be
diff --git a/lib/spack/spack/hooks/dotkit.py b/lib/spack/spack/hooks/dotkit.py
index 9123637356..a140646e04 100644
--- a/lib/spack/spack/hooks/dotkit.py
+++ b/lib/spack/spack/hooks/dotkit.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack.modules
 
diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py
index 627184cabd..bcbd68dfa0 100644
--- a/lib/spack/spack/hooks/extensions.py
+++ b/lib/spack/spack/hooks/extensions.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 import spack
diff --git a/lib/spack/spack/hooks/licensing.py b/lib/spack/spack/hooks/licensing.py
new file mode 100644
index 0000000000..0f63b0e05a
--- /dev/null
+++ b/lib/spack/spack/hooks/licensing.py
@@ -0,0 +1,160 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os
+
+import spack
+import llnl.util.tty as tty
+from llnl.util.filesystem import join_path
+
+
+def pre_install(pkg):
+    """This hook handles global license setup for licensed software."""
+    if pkg.license_required:
+        set_up_license(pkg)
+
+
+def set_up_license(pkg):
+    """Prompt the user, letting them know that a license is required.
+
+    For packages that rely on license files, a global license file is
+    created and opened for editing.
+
+    For packages that rely on environment variables to point to a
+    license, a warning message is printed.
+
+    For all other packages, documentation on how to set up a license
+    is printed."""
+
+    # If the license can be stored in a file, create one
+    if pkg.license_files:
+        license_path = pkg.global_license_file
+        if not os.path.exists(license_path):
+            # Create a new license file
+            write_license_file(pkg, license_path)
+            # Open up file in user's favorite $EDITOR for editing
+            spack.editor(license_path)
+            tty.msg("Added global license file %s" % license_path)
+        else:
+            # Use already existing license file
+            tty.msg("Found already existing license %s" % license_path)
+
+    # If not a file, what about an environment variable?
+    elif pkg.license_vars:
+        tty.warn("A license is required to use %s. Please set %s to the "
+                 "full pathname to the license file, or port@host if you"
+                 " store your license keys on a dedicated license server" %
+                 (pkg.name, ' or '.join(pkg.license_vars)))
+
+    # If not a file or variable, suggest a website for further info
+    elif pkg.license_url:
+        tty.warn("A license is required to use %s. See %s for details" %
+                 (pkg.name, pkg.license_url))
+
+    # If all else fails, you're on your own
+    else:
+        tty.warn("A license is required to use %s" % pkg.name)
+
+
+def write_license_file(pkg, license_path):
+    """Writes empty license file.
+
+    Comments give suggestions on alternative methods of
+    installing a license."""
+
+    comment = pkg.license_comment
+
+    # Global license directory may not already exist
+    if not os.path.exists(os.path.dirname(license_path)):
+        os.makedirs(os.path.dirname(license_path))
+    license = open(license_path, 'w')
+
+    # License files
+    license.write("""\
+{0} A license is required to use {1}.
+{0}
+{0} The recommended solution is to store your license key in this global
+{0} license file. After installation, the following symlink(s) will be
+{0} added to point to this file (relative to the installation prefix):
+{0}
+""".format(comment, pkg.name))
+
+    for filename in pkg.license_files:
+        license.write("{0}\t{1}\n".format(comment, filename))
+
+    license.write("{0}\n".format(comment))
+
+    # Environment variables
+    if pkg.license_vars:
+        license.write("""\
+{0} Alternatively, use one of the following environment variable(s):
+{0}
+""".format(comment))
+
+        for var in pkg.license_vars:
+            license.write("{0}\t{1}\n".format(comment, var))
+
+        license.write("""\
+{0}
+{0} If you choose to store your license in a non-standard location, you may
+{0} set one of these variable(s) to the full pathname to the license file, or
+{0} port@host if you store your license keys on a dedicated license server.
+{0} You will likely want to set this variable in a module file so that it
+{0} gets loaded every time someone tries to use {1}.
+{0}
+""".format(comment, pkg.name))
+
+    # Documentation
+    if pkg.license_url:
+        license.write("""\
+{0} For further information on how to acquire a license, please refer to:
+{0}
+{0}\t{1}
+{0}
+""".format(comment, pkg.license_url))
+
+    license.write("""\
+{0} You may enter your license below.
+
+""".format(comment))
+
+    license.close()
+
+
+def post_install(pkg):
+    """This hook symlinks local licenses to the global license for
+    licensed software."""
+    if pkg.license_required:
+        symlink_license(pkg)
+
+
+def symlink_license(pkg):
+    """Create local symlinks that point to the global license file."""
+    target = pkg.global_license_file
+    for filename in pkg.license_files:
+        link_name = join_path(pkg.prefix, filename)
+        if os.path.exists(target):
+            os.symlink(target, link_name)
+            tty.msg("Added local symlink %s to global license file" %
+                    link_name)
diff --git a/lib/spack/spack/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py
index d78adb576e..83d67ea225 100644
--- a/lib/spack/spack/hooks/sbang.py
+++ b/lib/spack/spack/hooks/sbang.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 
diff --git a/lib/spack/spack/hooks/tclmodule.py b/lib/spack/spack/hooks/tclmodule.py
index 8b315f27a2..2c88810c97 100644
--- a/lib/spack/spack/hooks/tclmodule.py
+++ b/lib/spack/spack/hooks/tclmodule.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack.modules
 
diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py
index 6981f69ac0..0bbcfba6b4 100644
--- a/lib/spack/spack/mirror.py
+++ b/lib/spack/spack/mirror.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This file contains code for creating spack mirror directories.  A
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index c27043db8c..d2b819e80a 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -1,173 +1,424 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-"""This module contains code for creating environment modules, which
-can include dotkits, tcl modules, lmod, and others.
-
-The various types of modules are installed by post-install hooks and
-removed after an uninstall by post-uninstall hooks.  This class
-consolidates the logic for creating an abstract description of the
-information that module systems need.  Currently that includes a
-number of directories to be appended to paths in the user's environment:
-
-  * /bin directories to be appended to PATH
-  * /lib* directories for LD_LIBRARY_PATH
-  * /include directories for CPATH
-  * /man* and /share/man* directories for MANPATH
-  * the package prefix for CMAKE_PREFIX_PATH
-
-This module also includes logic for coming up with unique names for
-the module files so that they can be found by the various
-shell-support files in $SPACK/share/spack/setup-env.*.
-
-Each hook in hooks/ implements the logic for writing its specific type
-of module file.
 """
-__all__ = ['EnvModule', 'Dotkit', 'TclModule']
+This module contains code for creating environment modules, which can include
+dotkits, tcl modules, lmod, and others.
+
+The various types of modules are installed by post-install hooks and removed
+after an uninstall by post-uninstall hooks. This class consolidates the logic
+for creating an abstract description of the information that module systems
+need.
 
+This module also includes logic for coming up with unique names for the module
+files so that they can be found by the various shell-support files in
+$SPACK/share/spack/setup-env.*.
+
+Each hook in hooks/ implements the logic for writing its specific type of
+module file.
+"""
+import copy
+import datetime
 import os
+import os.path
 import re
+import string
 import textwrap
-import shutil
-from glob import glob
 
 import llnl.util.tty as tty
+import spack
+import spack.config
 from llnl.util.filesystem import join_path, mkdirp
+from spack.build_environment import parent_class_modules
+from spack.build_environment import set_module_variables_for_package
+from spack.environment import *
 
-import spack
+__all__ = ['EnvModule', 'Dotkit', 'TclModule']
 
-"""Registry of all types of modules.  Entries created by EnvModule's
-   metaclass."""
+# Registry of all types of modules.  Entries created by EnvModule's metaclass
 module_types = {}
 
+CONFIGURATION = spack.config.get_config('modules')
 
-def print_help():
-    """For use by commands to tell user how to activate shell support."""
 
-    tty.msg("This command requires spack's shell integration.",
-            "",
+def print_help():
+    """
+    For use by commands to tell user how to activate shell support.
+    """
+    tty.msg("This command requires spack's shell integration.", "",
             "To initialize spack's shell commands, you must run one of",
             "the commands below.  Choose the right command for your shell.",
-            "",
-            "For bash and zsh:",
-            "    . %s/setup-env.sh" % spack.share_path,
-            "",
-            "For csh and tcsh:",
-            "    setenv SPACK_ROOT %s"    % spack.prefix,
-            "    source %s/setup-env.csh" % spack.share_path,
-            "")
+            "", "For bash and zsh:",
+            "    . %s/setup-env.sh" % spack.share_path, "",
+            "For csh and tcsh:", "    setenv SPACK_ROOT %s" % spack.prefix,
+            "    source %s/setup-env.csh" % spack.share_path, "")
+
+
+def inspect_path(prefix):
+    """
+    Inspects the prefix of an installation to search for common layouts. Issues
+    a request to modify the environment accordingly when an item is found.
+
+    Args:
+        prefix: prefix of the installation
+
+    Returns:
+        instance of EnvironmentModifications containing the requested
+        modifications
+    """
+    env = EnvironmentModifications()
+    # Inspect the prefix to check for the existence of common directories
+    prefix_inspections = CONFIGURATION.get('prefix_inspections', {})
+    for relative_path, variables in prefix_inspections.items():
+        expected = join_path(prefix, relative_path)
+        if os.path.isdir(expected):
+            for variable in variables:
+                env.prepend_path(variable, expected)
+    return env
+
+
+def dependencies(spec, request='all'):
+    """
+    Returns the list of dependent specs for a given spec, according to the
+    given request
+
+    Args:
+        spec: target spec
+        request: either 'none', 'direct' or 'all'
+
+    Returns:
+        empty list if 'none', direct dependency list if 'direct', all
+        dependencies if 'all'
+    """
+    if request not in ('none', 'direct', 'all'):
+        message = "Wrong value for argument 'request' : "
+        message += "should be one of ('none', 'direct', 'all')"
+        raise tty.error(message + " [current value is '%s']" % request)
+
+    if request == 'none':
+        return []
+
+    if request == 'direct':
+        return [xx for _, xx in spec.dependencies.items()]
+
+    # FIXME : during module file creation nodes seem to be visited multiple
+    # FIXME : times even if cover='nodes' is given. This work around permits
+    # FIXME : to get a unique list of spec anyhow. Do we miss a merge
+    # FIXME : step among nodes that refer to the same package?
+    seen = set()
+    seen_add = seen.add
+    l = [xx
+         for xx in sorted(
+             spec.traverse(order='post',
+                           depth=True,
+                           cover='nodes',
+                           root=False),
+             reverse=True)]
+    return [xx for ii, xx in l if not (xx in seen or seen_add(xx))]
+
+
+def update_dictionary_extending_lists(target, update):
+    for key in update:
+        value = target.get(key, None)
+        if isinstance(value, list):
+            target[key].extend(update[key])
+        elif isinstance(value, dict):
+            update_dictionary_extending_lists(target[key], update[key])
+        else:
+            target[key] = update[key]
+
+
+def parse_config_options(module_generator):
+    """
+    Parse the configuration file and returns a bunch of items that will be
+    needed during module file generation
+
+    Args:
+        module_generator: module generator for a given spec
+
+    Returns:
+        autoloads: list of specs to be autoloaded
+        prerequisites: list of specs to be marked as prerequisite
+        filters: list of environment variables whose modification is
+        blacklisted in module files
+        env: list of custom environment modifications to be applied in the
+        module file
+    """
+    # Get the configuration for this kind of generator
+    module_configuration = copy.deepcopy(CONFIGURATION.get(
+        module_generator.name, {}))
+
+    #####
+    # Merge all the rules
+    #####
+    module_file_actions = module_configuration.pop('all', {})
+    for spec, conf in module_configuration.items():
+        override = False
+        if spec.endswith(':'):
+            spec = spec.strip(':')
+            override = True
+        if module_generator.spec.satisfies(spec):
+            if override:
+                module_file_actions = {}
+            update_dictionary_extending_lists(module_file_actions, conf)
+
+    #####
+    # Process the common rules
+    #####
+
+    # Automatic loading loads
+    module_file_actions['autoload'] = dependencies(
+        module_generator.spec, module_file_actions.get('autoload', 'none'))
+    # Prerequisites
+    module_file_actions['prerequisites'] = dependencies(
+        module_generator.spec, module_file_actions.get('prerequisites',
+                                                       'none'))
+    # Environment modifications
+    environment_actions = module_file_actions.pop('environment', {})
+    env = EnvironmentModifications()
+
+    def process_arglist(arglist):
+        if method == 'unset':
+            for x in arglist:
+                yield (x, )
+        else:
+            for x in arglist.iteritems():
+                yield x
+
+    for method, arglist in environment_actions.items():
+        for args in process_arglist(arglist):
+            getattr(env, method)(*args)
+
+    return module_file_actions, env
+
+
+def filter_blacklisted(specs, module_name):
+    """
+    Given a sequence of specs, filters the ones that are blacklisted in the
+    module configuration file.
+
+    Args:
+        specs: sequence of spec instances
+        module_name: type of module file objects
+
+    Yields:
+        non blacklisted specs
+    """
+    for x in specs:
+        if module_types[module_name](x).blacklisted:
+            tty.debug('\tFILTER : %s' % x)
+            continue
+        yield x
 
 
 class EnvModule(object):
     name = 'env_module'
+    formats = {}
 
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module':
+            if cls.name != 'env_module' and cls.name in CONFIGURATION[
+                    'enable']:
                 module_types[cls.name] = cls
 
-
     def __init__(self, spec=None):
-        # category in the modules system
-        # TODO: come up with smarter category names.
-        self.category = "spack"
+        self.spec = spec
+        self.pkg = spec.package  # Just stored for convenience
 
-        # Descriptions for the module system's UI
-        self.short_description = ""
-        self.long_description = ""
+        # short description default is just the package + version
+        # packages can provide this optional attribute
+        self.short_description = spec.format("$_ $@")
+        if hasattr(self.pkg, 'short_description'):
+            self.short_description = self.pkg.short_description
 
-        # dict pathname -> list of directories to be prepended to in
-        # the module file.
-        self._paths = None
-        self.spec = spec
+        # long description is the docstring with reduced whitespace.
+        self.long_description = None
+        if self.spec.package.__doc__:
+            self.long_description = re.sub(r'\s+', ' ',
+                                           self.spec.package.__doc__)
+
+    @property
+    def naming_scheme(self):
+        try:
+            naming_scheme = CONFIGURATION[self.name]['naming_scheme']
+        except KeyError:
+            naming_scheme = self.default_naming_format
+        return naming_scheme
 
+    @property
+    def tokens(self):
+        tokens = {
+            'name': self.spec.name,
+            'version': self.spec.version,
+            'compiler': self.spec.compiler
+        }
+        return tokens
 
     @property
-    def paths(self):
-        if self._paths is None:
-            self._paths = {}
-
-            def add_path(path_name, directory):
-                path = self._paths.setdefault(path_name, [])
-                path.append(directory)
-
-            # Add paths if they exist.
-            for var, directory in [
-                    ('PATH', self.spec.prefix.bin),
-                    ('MANPATH', self.spec.prefix.man),
-                    ('MANPATH', self.spec.prefix.share_man),
-                    ('LIBRARY_PATH', self.spec.prefix.lib),
-                    ('LIBRARY_PATH', self.spec.prefix.lib64),
-                    ('LD_LIBRARY_PATH', self.spec.prefix.lib),
-                    ('LD_LIBRARY_PATH', self.spec.prefix.lib64),
-                    ('CPATH', self.spec.prefix.include),
-                    ('PKG_CONFIG_PATH', join_path(self.spec.prefix.lib, 'pkgconfig')),
-                    ('PKG_CONFIG_PATH', join_path(self.spec.prefix.lib64, 'pkgconfig'))]:
-
-                if os.path.isdir(directory):
-                    add_path(var, directory)
-
-            # Add python path unless it's an actual python installation
-            # TODO: is there a better way to do this?
-            if self.spec.name != 'python':
-                site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
-                if site_packages:
-                    add_path('PYTHONPATH', site_packages[0])
-
-            if self.spec.package.extends(spack.spec.Spec('ruby')):
-              add_path('GEM_PATH', self.spec.prefix)
-
-            # short description is just the package + version
-            # TODO: maybe packages can optionally provide it.
-            self.short_description = self.spec.format("$_ $@")
-
-            # long description is the docstring with reduced whitespace.
-            if self.spec.package.__doc__:
-                self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
-
-        return self._paths
+    def use_name(self):
+        """
+        Subclasses should implement this to return the name the module command
+        uses to refer to the package.
+        """
+        naming_tokens = self.tokens
+        naming_scheme = self.naming_scheme
+        name = naming_scheme.format(**naming_tokens)
+        name += '-' + self.spec.dag_hash(
+        )  # Always append the hash to make the module file unique
+        # Not everybody is working on linux...
+        parts = name.split('/')
+        name = join_path(*parts)
+        return name
 
+    @property
+    def category(self):
+        # Anything defined at the package level takes precedence
+        if hasattr(self.pkg, 'category'):
+            return self.pkg.category
+        # Extensions
+        for extendee in self.pkg.extendees:
+            return '{extendee}_extension'.format(extendee=extendee)
+        # Not very descriptive fallback
+        return 'spack'
+
+    @property
+    def blacklisted(self):
+        configuration = CONFIGURATION.get(self.name, {})
+        whitelist_matches = [x
+                             for x in configuration.get('whitelist', [])
+                             if self.spec.satisfies(x)]
+        blacklist_matches = [x
+                             for x in configuration.get('blacklist', [])
+                             if self.spec.satisfies(x)]
+        if whitelist_matches:
+            message = '\tWHITELIST : %s [matches : ' % self.spec.cshort_spec
+            for rule in whitelist_matches:
+                message += '%s ' % rule
+            message += ' ]'
+            tty.debug(message)
+
+        if blacklist_matches:
+            message = '\tBLACKLIST : %s [matches : ' % self.spec.cshort_spec
+            for rule in blacklist_matches:
+                message += '%s ' % rule
+            message += ' ]'
+            tty.debug(message)
+
+        if not whitelist_matches and blacklist_matches:
+            return True
+
+        return False
 
     def write(self):
-        """Write out a module file for this object."""
+        """
+        Writes out a module file for this object.
+
+        This method employs a template pattern and expects derived classes to:
+        - override the header property
+        - provide formats for autoload, prerequisites and environment changes
+        """
+        if self.blacklisted:
+            return
+        tty.debug("\tWRITE : %s [%s]" %
+                  (self.spec.cshort_spec, self.file_name))
+
         module_dir = os.path.dirname(self.file_name)
         if not os.path.exists(module_dir):
             mkdirp(module_dir)
 
-        # If there are no paths, no need for a dotkit.
-        if not self.paths:
-            return
-
+        # Environment modifications guessed by inspecting the
+        # installation prefix
+        env = inspect_path(self.spec.prefix)
+
+        # Let the extendee/dependency modify their extensions/dependencies
+        # before asking for package-specific modifications
+        spack_env = EnvironmentModifications()
+        # TODO : the code down below is quite similar to
+        # TODO : build_environment.setup_package and needs to be factored out
+        # TODO : to a single place
+        for item in dependencies(self.spec, 'all'):
+            package = self.spec[item.name].package
+            modules = parent_class_modules(package.__class__)
+            for mod in modules:
+                set_module_variables_for_package(package, mod)
+            set_module_variables_for_package(package, package.module)
+            package.setup_dependent_package(self.pkg.module, self.spec)
+            package.setup_dependent_environment(spack_env, env, self.spec)
+
+        # Package-specific environment modifications
+        set_module_variables_for_package(self.pkg, self.pkg.module)
+        self.spec.package.setup_environment(spack_env, env)
+
+        # Parse configuration file
+        module_configuration, conf_env = parse_config_options(self)
+        env.extend(conf_env)
+        filters = module_configuration.get('filter', {}).get(
+            'environment_blacklist', {})
+        # Build up the module file content
+        module_file_content = self.header
+        for x in filter_blacklisted(
+                module_configuration.pop('autoload', []), self.name):
+            module_file_content += self.autoload(x)
+        for x in filter_blacklisted(
+                module_configuration.pop('prerequisites', []), self.name):
+            module_file_content += self.prerequisite(x)
+        for line in self.process_environment_command(
+                filter_environment_blacklist(env, filters)):
+            module_file_content += line
+        for line in self.module_specific_content(module_configuration):
+            module_file_content += line
+
+        # Dump to file
         with open(self.file_name, 'w') as f:
-            self._write(f)
+            f.write(module_file_content)
 
-
-    def _write(self, stream):
-        """To be implemented by subclasses."""
+    @property
+    def header(self):
         raise NotImplementedError()
 
+    def module_specific_content(self, configuration):
+        return tuple()
+
+    def autoload(self, spec):
+        m = type(self)(spec)
+        return self.autoload_format.format(module_file=m.use_name)
+
+    def prerequisite(self, spec):
+        m = type(self)(spec)
+        return self.prerequisite_format.format(module_file=m.use_name)
+
+    def process_environment_command(self, env):
+        for command in env:
+            try:
+                yield self.environment_modifications_formats[type(
+                    command)].format(**command.args)
+            except KeyError:
+                message = 'Cannot handle command of type {command} : skipping request'  # NOQA: ignore=E501
+                details = '{context} at {filename}:{lineno}'
+                tty.warn(message.format(command=type(command)))
+                tty.warn(details.format(**command.args))
 
     @property
     def file_name(self):
@@ -175,94 +426,127 @@ class EnvModule(object):
            where this module lives."""
         raise NotImplementedError()
 
-
-    @property
-    def use_name(self):
-        """Subclasses should implement this to return the name the
-           module command uses to refer to the package."""
-        raise NotImplementedError()
-
-
     def remove(self):
         mod_file = self.file_name
         if os.path.exists(mod_file):
-            shutil.rmtree(mod_file, ignore_errors=True)
+            try:
+                os.remove(mod_file)  # Remove the module file
+                os.removedirs(
+                    os.path.dirname(mod_file)
+                )  # Remove all the empty directories from the leaf up
+            except OSError:
+                # removedirs throws OSError on first non-empty directory found
+                pass
 
 
 class Dotkit(EnvModule):
     name = 'dotkit'
     path = join_path(spack.share_path, "dotkit")
 
+    environment_modifications_formats = {
+        PrependPath: 'dk_alter {name} {value}\n',
+        SetEnv: 'dk_setenv {name} {value}\n'
+    }
+
+    autoload_format = 'dk_op {module_file}\n'
+
+    default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}'  # NOQA: ignore=E501
+
     @property
     def file_name(self):
         return join_path(Dotkit.path, self.spec.architecture,
                          '%s.dk' % self.use_name)
 
     @property
-    def use_name(self):
-      return "%s-%s-%s-%s-%s" % (self.spec.name, self.spec.version,
-                                 self.spec.compiler.name,
-                                 self.spec.compiler.version, 
-                                 self.spec.dag_hash())
-
-    def _write(self, dk_file):
+    def header(self):
         # Category
+        header = ''
         if self.category:
-            dk_file.write('#c %s\n' % self.category)
+            header += '#c %s\n' % self.category
 
         # Short description
         if self.short_description:
-            dk_file.write('#d %s\n' % self.short_description)
+            header += '#d %s\n' % self.short_description
 
         # Long description
         if self.long_description:
             for line in textwrap.wrap(self.long_description, 72):
-                dk_file.write("#h %s\n" % line)
+                header += '#h %s\n' % line
+        return header
 
-        # Path alterations
-        for var, dirs in self.paths.items():
-            for directory in dirs:
-                dk_file.write("dk_alter %s %s\n" % (var, directory))
-
-        # Let CMake find this package.
-        dk_file.write("dk_alter CMAKE_PREFIX_PATH %s\n" % self.spec.prefix)
+    def prerequisite(self, spec):
+        tty.warn('prerequisites:  not supported by dotkit module files')
+        tty.warn('\tYou may want to check  ~/.spack/modules.yaml')
+        return ''
 
 
 class TclModule(EnvModule):
     name = 'tcl'
     path = join_path(spack.share_path, "modules")
 
-    @property
-    def file_name(self):
-        return join_path(TclModule.path, self.spec.architecture, self.use_name)
+    environment_modifications_formats = {
+        PrependPath: 'prepend-path --delim "{delim}" {name} \"{value}\"\n',
+        AppendPath: 'append-path   --delim "{delim}" {name} \"{value}\"\n',
+        RemovePath: 'remove-path   --delim "{delim}" {name} \"{value}\"\n',
+        SetEnv: 'setenv {name} \"{value}\"\n',
+        UnsetEnv: 'unsetenv {name}\n'
+    }
 
+    autoload_format = ('if ![ is-loaded {module_file} ] {{\n'
+                       '    puts stderr "Autoloading {module_file}"\n'
+                       '    module load {module_file}\n'
+                       '}}\n\n')
 
-    @property
-    def use_name(self):
-      return "%s-%s-%s-%s-%s" % (self.spec.name, self.spec.version,
-                                 self.spec.compiler.name,
-                                 self.spec.compiler.version, 
-                                 self.spec.dag_hash())
+    prerequisite_format = 'prereq {module_file}\n'
 
+    default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}'  # NOQA: ignore=E501
 
-    def _write(self, m_file):
-        # TODO: cateogry?
-        m_file.write('#%Module1.0\n')
+    @property
+    def file_name(self):
+        return join_path(TclModule.path, self.spec.architecture, self.use_name)
 
+    @property
+    def header(self):
+        timestamp = datetime.datetime.now()
+        # TCL Modulefile header
+        header = '#%Module1.0\n'
+        header += '## Module file created by spack (https://github.com/LLNL/spack) on %s\n' % timestamp  # NOQA: ignore=E501
+        header += '##\n'
+        header += '## %s\n' % self.spec.short_spec
+        header += '##\n'
+
+        # TODO : category ?
         # Short description
         if self.short_description:
-            m_file.write('module-whatis \"%s\"\n\n' % self.short_description)
+            header += 'module-whatis \"%s\"\n\n' % self.short_description
 
         # Long description
         if self.long_description:
-            m_file.write('proc ModulesHelp { } {\n')
-            doc = re.sub(r'"', '\"', self.long_description)
-            m_file.write("puts stderr \"%s\"\n" % doc)
-            m_file.write('}\n\n')
-
-        # Path alterations
-        for var, dirs in self.paths.items():
-            for directory in dirs:
-                m_file.write("prepend-path %s \"%s\"\n" % (var, directory))
-
-        m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix)
+            header += 'proc ModulesHelp { } {\n'
+            for line in textwrap.wrap(self.long_description, 72):
+                header += 'puts stderr "%s"\n' % line
+            header += '}\n\n'
+        return header
+
+    def module_specific_content(self, configuration):
+        naming_tokens = self.tokens
+        # Conflict
+        conflict_format = configuration.get('conflict', [])
+        f = string.Formatter()
+        for item in conflict_format:
+            line = 'conflict ' + item + '\n'
+            if len([x for x in f.parse(line)
+                    ]) > 1:  # We do have placeholder to substitute
+                for naming_dir, conflict_dir in zip(
+                        self.naming_scheme.split('/'), item.split('/')):
+                    if naming_dir != conflict_dir:
+                        message = 'conflict scheme does not match naming scheme [{spec}]\n\n'  # NOQA: ignore=E501
+                        message += 'naming scheme   : "{nformat}"\n'
+                        message += 'conflict scheme : "{cformat}"\n\n'
+                        message += '** You may want to check your `modules.yaml` configuration file **\n'  # NOQA: ignore=E501
+                        tty.error(message.format(spec=self.spec,
+                                                 nformat=self.naming_scheme,
+                                                 cformat=item))
+                        raise SystemExit('Module generation aborted.')
+                line = line.format(**naming_tokens)
+            yield line
diff --git a/lib/spack/spack/multimethod.py b/lib/spack/spack/multimethod.py
index 3cd17e796a..170ef3cea2 100644
--- a/lib/spack/spack/multimethod.py
+++ b/lib/spack/spack/multimethod.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """This module contains utilities for using multi-methods in
 spack. You can think of multi-methods like overloaded methods --
@@ -146,12 +146,12 @@ class when(object):
               def install(self, prefix):
                   # Do default install
 
-              @when('=chaos_5_x86_64_ib')
+              @when('arch=chaos_5_x86_64_ib')
               def install(self, prefix):
                   # This will be executed instead of the default install if
                   # the package's sys_type() is chaos_5_x86_64_ib.
 
-              @when('=bgqos_0")
+              @when('arch=bgqos_0")
               def install(self, prefix):
                   # This will be executed if the package's sys_type is bgqos_0
 
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 1da9af753c..0edb70e4ca 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This is where most of the action happens in Spack.
@@ -34,41 +34,33 @@ rundown on spack and how it differs from homebrew, look at the
 README.
 """
 import os
-import errno
 import re
-import shutil
-import time
-import itertools
-import subprocess
-import platform as py_platform
-import multiprocessing
-from urlparse import urlparse, urljoin
 import textwrap
-from StringIO import StringIO
+import time
 
 import llnl.util.tty as tty
-from llnl.util.tty.log import log_output
-from llnl.util.link_tree import LinkTree
-from llnl.util.filesystem import *
-from llnl.util.lang import *
-
 import spack
-import spack.error
+import spack.build_environment
 import spack.compilers
-import spack.mirror
-import spack.hooks
 import spack.directives
+import spack.error
+import spack.fetch_strategy as fs
+import spack.hooks
+import spack.mirror
 import spack.repository
-import spack.build_environment
 import spack.url
 import spack.util.web
-import spack.fetch_strategy as fs
-from spack.version import *
+from StringIO import StringIO
+from llnl.util.filesystem import *
+from llnl.util.lang import *
+from llnl.util.link_tree import LinkTree
+from llnl.util.tty.log import log_output
 from spack.stage import Stage, ResourceStage, StageComposite
-from spack.util.compression import allowed_archive, extension
-from spack.util.executable import ProcessError
+from spack.util.compression import allowed_archive
 from spack.util.environment import dump_environment
-
+from spack.util.executable import ProcessError
+from spack.version import *
+from urlparse import urlparse
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
 
@@ -311,13 +303,20 @@ class Package(object):
     #
     """By default we build in parallel.  Subclasses can override this."""
     parallel = True
-
     """# jobs to use for parallel make. If set, overrides default of ncpus."""
     make_jobs = None
-
-    """Most packages are NOT extendable.  Set to True if you want extensions."""
+    """Most packages are NOT extendable. Set to True if you want extensions."""
     extendable = False
-
+    """List of prefix-relative file paths (or a single path). If these do
+       not exist after install, or if they exist but are not files,
+       sanity checks fail.
+    """
+    sanity_check_is_file = []
+    """List of prefix-relative directory paths (or a single path). If
+       these do not exist after install, or if they exist but are not
+       directories, sanity checks will fail.
+    """
+    sanity_check_is_dir = []
 
     def __init__(self, spec):
         # this determines how the package should be built.
@@ -329,21 +328,25 @@ class Package(object):
         if '.' in self.name:
             self.name = self.name[self.name.rindex('.') + 1:]
 
+        # Allow custom staging paths for packages
+        self.path = None
+
         # Sanity check attributes required by Spack directives.
         spack.directives.ensure_dicts(type(self))
 
         # Check versions in the versions dict.
         for v in self.versions:
-            assert(isinstance(v, Version))
+            assert (isinstance(v, Version))
 
         # Check version descriptors
         for v in sorted(self.versions):
-            assert(isinstance(self.versions[v], dict))
+            assert (isinstance(self.versions[v], dict))
 
         # Version-ize the keys in versions dict
         try:
-            self.versions = dict((Version(v), h) for v,h in self.versions.items())
-        except ValueError, e:
+            self.versions = dict((Version(v), h)
+                                 for v, h in self.versions.items())
+        except ValueError as e:
             raise ValueError("In package %s: %s" % (self.name, e.message))
 
         # stage used to build this package.
@@ -357,9 +360,9 @@ class Package(object):
         # This makes self.url behave sanely.
         if self.spec.versions.concrete:
             # TODO: this is a really roundabout way of determining the type
-            # TODO: of fetch to do. figure out a more sane fetch strategy/package
-            # TODO: init order (right now it's conflated with stage, package, and
-            # TODO: the tests make assumptions)
+            # TODO: of fetch to do. figure out a more sane fetch
+            # TODO: strategy/package init order (right now it's conflated with
+            # TODO: stage, package, and the tests make assumptions)
             f = fs.for_package_version(self, self.version)
             if isinstance(f, fs.URLFetchStrategy):
                 self.url = self.url_for_version(self.spec.version)
@@ -371,6 +374,22 @@ class Package(object):
         if not hasattr(self, 'list_depth'):
             self.list_depth = 1
 
+        # Set default licensing information
+        if not hasattr(self, 'license_required'):
+            self.license_required = False
+
+        if not hasattr(self, 'license_comment'):
+            self.license_comment = '#'
+
+        if not hasattr(self, 'license_files'):
+            self.license_files = []
+
+        if not hasattr(self, 'license_vars'):
+            self.license_vars = []
+
+        if not hasattr(self, 'license_url'):
+            self.license_url = None
+
         # Set up some internal variables for timing.
         self._fetch_time = 0.0
         self._total_time = 0.0
@@ -378,6 +397,15 @@ class Package(object):
         if self.is_extension:
             spack.repo.get(self.extendee_spec)._check_extendable()
 
+    @property
+    def global_license_file(self):
+        """Returns the path where a global license file should be stored."""
+        if not self.license_files:
+            return
+        spack_root = ancestor(__file__, 4)
+        global_license_dir = join_path(spack_root, 'etc', 'spack', 'licenses')
+        return join_path(global_license_dir, self.name,
+                         os.path.basename(self.license_files[0]))
 
     @property
     def version(self):
@@ -385,7 +413,6 @@ class Package(object):
             raise ValueError("Can only get of package with concrete version.")
         return self.spec.versions[0]
 
-
     @memoized
     def version_urls(self):
         """Return a list of URLs for different versions of this
@@ -398,7 +425,6 @@ class Package(object):
                 version_urls[v] = args['url']
         return version_urls
 
-
     def nearest_url(self, version):
         """Finds the URL for the next lowest version with a URL.
            If there is no lower version with a URL, uses the
@@ -415,10 +441,11 @@ class Package(object):
                 url = version_urls[v]
         return url
 
-
     # TODO: move this out of here and into some URL extrapolation module?
     def url_for_version(self, version):
-        """Returns a URL that you can download a new version of this package from."""
+        """
+        Returns a URL that you can download a new version of this package from.
+        """
         if not isinstance(version, Version):
             version = Version(version)
 
@@ -432,14 +459,18 @@ class Package(object):
             return version_urls[version]
 
         # If we have no idea, try to substitute the version.
-        return spack.url.substitute_version(self.nearest_url(version),
-                                            self.url_version(version))
+        return spack.url.substitute_version(
+            self.nearest_url(version), self.url_version(version))
 
     def _make_resource_stage(self, root_stage, fetcher, resource):
         resource_stage_folder = self._resource_stage(resource)
         resource_mirror = join_path(self.name, os.path.basename(fetcher.url))
-        stage = ResourceStage(resource.fetcher, root=root_stage, resource=resource,
-                              name=resource_stage_folder, mirror_path=resource_mirror)
+        stage = ResourceStage(resource.fetcher,
+                              root=root_stage,
+                              resource=resource,
+                              name=resource_stage_folder,
+                              mirror_path=resource_mirror,
+                              path=self.path)
         return stage
 
     def _make_root_stage(self, fetcher):
@@ -449,7 +480,7 @@ class Package(object):
         s = self.spec
         stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash())
         # Build the composite stage
-        stage = Stage(fetcher, mirror_path=mp, name=stage_name)
+        stage = Stage(fetcher, mirror_path=mp, name=stage_name, path=self.path)
         return stage
 
     def _make_stage(self):
@@ -464,7 +495,8 @@ class Package(object):
             else:
                 # Construct resource stage
                 resource = resources[ii - 1]  # ii == 0 is root!
-                stage = self._make_resource_stage(composite_stage[0], fetcher, resource)
+                stage = self._make_resource_stage(composite_stage[0], fetcher,
+                                                  resource)
             # Append the item to the composite
             composite_stage.append(stage)
 
@@ -482,13 +514,11 @@ class Package(object):
             self._stage = self._make_stage()
         return self._stage
 
-
     @stage.setter
     def stage(self, stage):
         """Allow a stage object to be set to override the default."""
         self._stage = stage
 
-
     def _make_fetcher(self):
         # Construct a composite fetcher that always contains at least
         # one element (the root package). In case there are resources
@@ -505,7 +535,8 @@ class Package(object):
     @property
     def fetcher(self):
         if not self.spec.versions.concrete:
-            raise ValueError("Can only get a fetcher for a package with concrete versions.")
+            raise ValueError(
+                "Can only get a fetcher for a package with concrete versions.")
         if not self._fetcher:
             self._fetcher = self._make_fetcher()
         return self._fetcher
@@ -514,10 +545,11 @@ class Package(object):
     def fetcher(self, f):
         self._fetcher = f
 
-
     @property
     def extendee_spec(self):
-        """Spec of the extendee of this package, or None if it is not an extension."""
+        """
+        Spec of the extendee of this package, or None if it is not an extension
+        """
         if not self.extendees:
             return None
 
@@ -539,10 +571,11 @@ class Package(object):
             spec, kwargs = self.extendees[name]
             return spec
 
-
     @property
     def extendee_args(self):
-        """Spec of the extendee of this package, or None if it is not an extension."""
+        """
+        Spec of the extendee of this package, or None if it is not an extension
+        """
         if not self.extendees:
             return None
 
@@ -550,7 +583,6 @@ class Package(object):
         name = next(iter(self.extendees))
         return self.extendees[name][1]
 
-
     @property
     def is_extension(self):
         # if it is concrete, it's only an extension if it actually
@@ -561,22 +593,20 @@ class Package(object):
             # If not, then it's an extension if it *could* be an extension
             return bool(self.extendees)
 
-
     def extends(self, spec):
-        if not spec.name in self.extendees:
+        if spec.name not in self.extendees:
             return False
         s = self.extendee_spec
         return s and s.satisfies(spec)
 
-
     @property
     def activated(self):
         if not self.is_extension:
-            raise ValueError("is_extension called on package that is not an extension.")
+            raise ValueError(
+                "is_extension called on package that is not an extension.")
         exts = spack.install_layout.extension_map(self.extendee_spec)
         return (self.name in exts) and (exts[self.name] == self.spec)
 
-
     def preorder_traversal(self, visited=None, **kwargs):
         """This does a preorder traversal of the package's dependence DAG."""
         virtual = kwargs.get("virtual", False)
@@ -595,36 +625,35 @@ class Package(object):
             spec = self.dependencies[name]
 
             # currently, we do not descend into virtual dependencies, as this
-            # makes doing a sensible traversal much harder.  We just assume that
-            # ANY of the virtual deps will work, which might not be true (due to
-            # conflicts or unsatisfiable specs).  For now this is ok but we might
-            # want to reinvestigate if we start using a lot of complicated virtual
-            # dependencies
+            # makes doing a sensible traversal much harder.  We just assume
+            # that ANY of the virtual deps will work, which might not be true
+            # (due to conflicts or unsatisfiable specs).  For now this is ok
+            # but we might want to reinvestigate if we start using a lot of
+            # complicated virtual dependencies
             # TODO: reinvestigate this.
             if spec.virtual:
                 if virtual:
                     yield spec
                 continue
 
-            for pkg in spack.repo.get(name).preorder_traversal(visited, **kwargs):
+            for pkg in spack.repo.get(name).preorder_traversal(visited,
+                                                               **kwargs):
                 yield pkg
 
-
     def provides(self, vpkg_name):
-        """True if this package provides a virtual package with the specified name."""
+        """
+        True if this package provides a virtual package with the specified name
+        """
         return any(s.name == vpkg_name for s in self.provided)
 
-
     def virtual_dependencies(self, visited=None):
         for spec in sorted(set(self.preorder_traversal(virtual=True))):
             yield spec
 
-
     @property
     def installed(self):
         return os.path.isdir(self.prefix)
 
-
     @property
     def installed_dependents(self):
         """Return a list of the specs of all installed packages that depend
@@ -641,62 +670,64 @@ class Package(object):
                     dependents.append(spec)
         return dependents
 
-
     @property
     def prefix(self):
         """Get the prefix into which this package should be installed."""
         return self.spec.prefix
 
-
     @property
     #TODO: Change this to architecture
     def compiler(self):
-        """Get the spack.compiler.Compiler object used to build this package."""
+        """Get the spack.compiler.Compiler object used to build this package"""
         if not self.spec.concrete:
             raise ValueError("Can only get a compiler for a concrete package.")
         return spack.compilers.compiler_for_spec(self.spec.compiler, 
                 self.spec.architecture.platform_os)
 
-
     def url_version(self, version):
-        """Given a version, this returns a string that should be substituted into the
-           package's URL to download that version.
-           By default, this just returns the version string. Subclasses may need to
-           override this, e.g. for boost versions where you need to ensure that there
-           are _'s in the download URL.
         """
-        return str(version)
+        Given a version, this returns a string that should be substituted
+        into the package's URL to download that version.
 
+        By default, this just returns the version string. Subclasses may need
+        to override this, e.g. for boost versions where you need to ensure that
+        there are _'s in the download URL.
+        """
+        return str(version)
 
     def remove_prefix(self):
-        """Removes the prefix for a package along with any empty parent directories."""
+        """
+        Removes the prefix for a package along with any empty parent
+        directories
+        """
         spack.install_layout.remove_install_directory(self.spec)
 
-
     def do_fetch(self, mirror_only=False):
-        """Creates a stage directory and downloads the tarball for this package.
-           Working directory will be set to the stage directory.
+        """
+        Creates a stage directory and downloads the tarball for this package.
+        Working directory will be set to the stage directory.
         """
         if not self.spec.concrete:
             raise ValueError("Can only fetch concrete packages.")
 
         start_time = time.time()
-        if spack.do_checksum and not self.version in self.versions:
-            tty.warn("There is no checksum on file to fetch %s safely."
-                     % self.spec.format('$_$@'))
+        if spack.do_checksum and self.version not in self.versions:
+            tty.warn("There is no checksum on file to fetch %s safely." %
+                     self.spec.format('$_$@'))
 
             # Ask the user whether to skip the checksum if we're
             # interactive, but just fail if non-interactive.
-            checksum_msg = "Add a checksum or use --no-checksum to skip this check."
+            checksum_msg = "Add a checksum or use --no-checksum to skip this check."  # NOQA: ignore=E501
             ignore_checksum = False
             if sys.stdout.isatty():
-                ignore_checksum = tty.get_yes_or_no("  Fetch anyway?", default=False)
+                ignore_checksum = tty.get_yes_or_no("  Fetch anyway?",
+                                                    default=False)
                 if ignore_checksum:
                     tty.msg("Fetching with no checksum.", checksum_msg)
 
             if not ignore_checksum:
-                raise FetchError(
-                    "Will not fetch %s" % self.spec.format('$_$@'), checksum_msg)
+                raise FetchError("Will not fetch %s" %
+                                 self.spec.format('$_$@'), checksum_msg)
 
         self.stage.fetch(mirror_only)
 
@@ -705,7 +736,6 @@ class Package(object):
         if spack.do_checksum and self.version in self.versions:
             self.stage.check()
 
-
     def do_stage(self, mirror_only=False):
         """Unpacks the fetched tarball, then changes into the expanded tarball
            directory."""
@@ -716,7 +746,6 @@ class Package(object):
         self.stage.expand_archive()
         self.stage.chdir_to_source()
 
-
     def do_patch(self):
         """Calls do_stage(), then applied patches to the expanded tarball if they
            haven't been applied already."""
@@ -736,10 +765,10 @@ class Package(object):
 
         # Construct paths to special files in the archive dir used to
         # keep track of whether patches were successfully applied.
-        archive_dir     = self.stage.source_path
-        good_file       = join_path(archive_dir, '.spack_patched')
+        archive_dir = self.stage.source_path
+        good_file = join_path(archive_dir, '.spack_patched')
         no_patches_file = join_path(archive_dir, '.spack_no_patches')
-        bad_file        = join_path(archive_dir, '.spack_patch_failed')
+        bad_file = join_path(archive_dir, '.spack_patch_failed')
 
         # If we encounter an archive that failed to patch, restage it
         # so that we can apply all the patches again.
@@ -794,13 +823,11 @@ class Package(object):
         else:
             touch(no_patches_file)
 
-
     @property
     def namespace(self):
         namespace, dot, module = self.__module__.rpartition('.')
         return namespace
 
-
     def do_fake_install(self):
         """Make a fake install directory contaiing a 'fake' file in bin."""
         mkdirp(self.prefix.bin)
@@ -808,15 +835,15 @@ class Package(object):
         mkdirp(self.prefix.lib)
         mkdirp(self.prefix.man1)
 
-
     def _get_needed_resources(self):
         resources = []
         # Select the resources that are needed for this build
         for when_spec, resource_list in self.resources.items():
             if when_spec in self.spec:
                 resources.extend(resource_list)
-        # Sorts the resources by the length of the string representing their destination. Since any nested resource
-        # must contain another resource's name in its path, it seems that should work
+        # Sorts the resources by the length of the string representing their
+        # destination. Since any nested resource must contain another
+        # resource's name in its path, it seems that should work
         resources = sorted(resources, key=lambda res: len(res.destination))
         return resources
 
@@ -825,10 +852,15 @@ class Package(object):
         resource_stage_folder = '-'.join(pieces)
         return resource_stage_folder
 
-
     def do_install(self,
-                   keep_prefix=False,  keep_stage=False, ignore_deps=False,
-                   skip_patch=False, verbose=False, make_jobs=None, fake=False):
+                   keep_prefix=False,
+                   keep_stage=False,
+                   ignore_deps=False,
+                   skip_patch=False,
+                   verbose=False,
+                   make_jobs=None,
+                   fake=False,
+                   explicit=False):
         """Called by commands to install a package and its dependencies.
 
         Package implementations should override install() to describe
@@ -839,32 +871,43 @@ class Package(object):
         keep_stage  -- By default, stage is destroyed only if there are no
                        exceptions during build. Set to True to keep the stage
                        even with exceptions.
-        ignore_deps -- Do not install dependencies before installing this package.
+        ignore_deps -- Don't install dependencies before installing this
+                       package
         fake        -- Don't really build -- install fake stub files instead.
         skip_patch  -- Skip patch stage of build if True.
         verbose     -- Display verbose build output (by default, suppresses it)
-        make_jobs   -- Number of make jobs to use for install.  Default is ncpus.
+        make_jobs   -- Number of make jobs to use for install. Default is ncpus
         """
         if not self.spec.concrete:
             raise ValueError("Can only install concrete packages.")
 
         # No installation needed if package is external
         if self.spec.external:
-            tty.msg("%s is externally installed in %s" % (self.name, self.spec.external))
+            tty.msg("%s is externally installed in %s" %
+                    (self.name, self.spec.external))
             return
 
         # Ensure package is not already installed
         if spack.install_layout.check_installed(self.spec):
             tty.msg("%s is already installed in %s" % (self.name, self.prefix))
+            rec = spack.installed_db.get_record(self.spec)
+            if (not rec.explicit) and explicit:
+                with spack.installed_db.write_transaction():
+                    rec = spack.installed_db.get_record(self.spec)
+                    rec.explicit = True
             return
 
         tty.msg("Installing %s" % self.name)
 
         # First, install dependencies recursively.
         if not ignore_deps:
-            self.do_install_dependencies(
-                keep_prefix=keep_prefix, keep_stage=keep_stage, ignore_deps=ignore_deps,
-                fake=fake, skip_patch=skip_patch, verbose=verbose, make_jobs=make_jobs)
+            self.do_install_dependencies(keep_prefix=keep_prefix,
+                                         keep_stage=keep_stage,
+                                         ignore_deps=ignore_deps,
+                                         fake=fake,
+                                         skip_patch=skip_patch,
+                                         verbose=verbose,
+                                         make_jobs=make_jobs)
 
         # Set parallelism before starting build.
         self.make_jobs = make_jobs
@@ -873,6 +916,7 @@ class Package(object):
         def build_process():
             """Forked for each build. Has its own process and python
                module space set up by build_environment.fork()."""
+
             start_time = time.time()
             if not fake:
                 if not skip_patch:
@@ -892,43 +936,53 @@ class Package(object):
                     self.do_fake_install()
                 else:
                     # Do the real install in the source directory.
-                     self.stage.chdir_to_source()
+                    self.stage.chdir_to_source()
 
-                     # Save the build environment in a file before building.
-                     env_path = join_path(os.getcwd(), 'spack-build.env')
+                    # Save the build environment in a file before building.
+                    env_path = join_path(os.getcwd(), 'spack-build.env')
 
-                     try:
-                        # Redirect I/O to a build log (and optionally to the terminal)
+                    try:
+                        # Redirect I/O to a build log (and optionally to
+                        # the terminal)
                         log_path = join_path(os.getcwd(), 'spack-build.out')
                         log_file = open(log_path, 'w')
-                        with log_output(log_file, verbose, sys.stdout.isatty(), True):
+                        with log_output(log_file, verbose, sys.stdout.isatty(),
+                                        True):
                             dump_environment(env_path)
                             self.install(self.spec, self.prefix)
 
-                     except ProcessError as e:
-                         # Annotate ProcessErrors with the location of the build log.
-                         e.build_log = log_path
-                         raise e
+                    except ProcessError as e:
+                        # Annotate ProcessErrors with the location of
+                        # the build log
+                        e.build_log = log_path
+                        raise e
+
+                    # Ensure that something was actually installed.
+                    self.sanity_check_prefix()
 
-                     # Ensure that something was actually installed.
-                     self._sanity_check_install()
+                    # Copy provenance into the install directory on success
+                    log_install_path = spack.install_layout.build_log_path(
+                        self.spec)
+                    env_install_path = spack.install_layout.build_env_path(
+                        self.spec)
+                    packages_dir = spack.install_layout.build_packages_path(
+                        self.spec)
 
-                     # Copy provenance into the install directory on success
-                     log_install_path = spack.install_layout.build_log_path(self.spec)
-                     env_install_path = spack.install_layout.build_env_path(self.spec)
-                     packages_dir = spack.install_layout.build_packages_path(self.spec)
+                    install(log_path, log_install_path)
+                    install(env_path, env_install_path)
+                    dump_packages(self.spec, packages_dir)
 
-                     install(log_path, log_install_path)
-                     install(env_path, env_install_path)
-                     dump_packages(self.spec, packages_dir)
+                # Run post install hooks before build stage is removed.
+                spack.hooks.post_install(self)
 
             # Stop timer.
             self._total_time = time.time() - start_time
             build_time = self._total_time - self._fetch_time
 
             tty.msg("Successfully installed %s" % self.name,
-                    "Fetch: %s.  Build: %s.  Total: %s."
-                    % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
+                    "Fetch: %s.  Build: %s.  Total: %s." %
+                    (_hms(self._fetch_time), _hms(build_time),
+                     _hms(self._total_time)))
             print_pkg(self.prefix)
 
         try:
@@ -943,31 +997,42 @@ class Package(object):
                 tty.warn("Keeping install prefix in place despite error.",
                          "Spack will think this package is installed. " +
                          "Manually remove this directory to fix:",
-                         self.prefix, wrap=True)
+                         self.prefix,
+                         wrap=True)
             raise
 
         # note: PARENT of the build process adds the new package to
         # the database, so that we don't need to re-read from file.
-        spack.installed_db.add(self.spec, self.prefix)
+        spack.installed_db.add(self.spec, self.prefix, explicit=explicit)
 
-        # Once everything else is done, run post install hooks
-        spack.hooks.post_install(self)
+    def sanity_check_prefix(self):
+        """This function checks whether install succeeded."""
 
+        def check_paths(path_list, filetype, predicate):
+            if isinstance(path_list, basestring):
+                path_list = [path_list]
+
+            for path in path_list:
+                abs_path = os.path.join(self.prefix, path)
+                if not predicate(abs_path):
+                    raise InstallError(
+                        "Install failed for %s. No such %s in prefix: %s" %
+                        (self.name, filetype, path))
+
+        check_paths(self.sanity_check_is_file, 'file', os.path.isfile)
+        check_paths(self.sanity_check_is_dir, 'directory', os.path.isdir)
 
-    def _sanity_check_install(self):
         installed = set(os.listdir(self.prefix))
         installed.difference_update(spack.install_layout.hidden_file_paths)
         if not installed:
             raise InstallError(
                 "Install failed for %s.  Nothing was installed!" % self.name)
 
-
     def do_install_dependencies(self, **kwargs):
         # Pass along paths of dependencies here
         for dep in self.spec.dependencies.values():
             dep.package.do_install(**kwargs)
 
-
     @property
     def build_log_path(self):
         if self.installed:
@@ -975,7 +1040,6 @@ class Package(object):
         else:
             return join_path(self.stage.source_path, 'spack-build.out')
 
-
     @property
     def module(self):
         """Use this to add variables to the class's module's scope.
@@ -984,37 +1048,127 @@ class Package(object):
         return __import__(self.__class__.__module__,
                           fromlist=[self.__class__.__name__])
 
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environments for a package.
+
+        `spack_env` and `run_env` are `EnvironmentModifications`
+        objects.  Package authors can call methods on them to alter
+        the environment within Spack and at runtime.
 
-    def setup_dependent_environment(self, module, spec, dependent_spec):
-        """Called before the install() method of dependents.
+        Both `spack_env` and `run_env` are applied within the build
+        process, before this package's `install()` method is called.
+
+        Modifications in `run_env` will *also* be added to the
+        generated environment modules for this package.
 
         Default implementation does nothing, but this can be
-        overridden by an extendable package to set up the install
-        environment for its extensions.  This is useful if there are
-        some common steps to installing all extensions for a
-        certain package.
+        overridden if the package needs a particular environment.
 
-        Some examples:
+        Examples:
 
-        1. Installing python modules generally requires PYTHONPATH to
-           point to the lib/pythonX.Y/site-packages directory in the
-           module's install prefix.  This could set that variable.
+            1. Qt extensions need `QTDIR` set.
 
-        2. Extensions often need to invoke the 'python' interpreter
-           from the Python installation being extended.  This routine can
-           put a 'python' Execuable object in the module scope for the
-           extension package to simplify extension installs.
+        Args:
+            spack_env (EnvironmentModifications): list of
+                modifications to be applied when this package is built
+                within Spack.
 
-        3. A lot of Qt extensions need QTDIR set.  This can be used to do that.
+            run_env (EnvironmentModifications): list of environment
+                changes to be applied when this package is run outside
+                of Spack.
 
         """
         pass
 
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        """Set up the environment of packages that depend on this one.
 
-    def install(self, spec, prefix):
-        """Package implementations override this with their own build configuration."""
-        raise InstallError("Package %s provides no install method!" % self.name)
+        This is similar to `setup_environment`, but it is used to
+        modify the compile and runtime environments of packages that
+        *depend* on this one. This gives packages like Python and
+        others that follow the extension model a way to implement
+        common environment or compile-time settings for dependencies.
+
+        By default, this delegates to self.setup_environment()
+
+        Example :
+
+            1. Installing python modules generally requires
+              `PYTHONPATH` to point to the lib/pythonX.Y/site-packages
+              directory in the module's install prefix.  This could
+              set that variable.
+
+        Args:
+
+            spack_env (EnvironmentModifications): list of
+                modifications to be applied when the dependent package
+                is bulit within Spack.
+
+            run_env (EnvironmentModifications): list of environment
+                changes to be applied when the dependent package is
+                run outside of Spack.
 
+            dependent_spec (Spec): The spec of the dependent package
+                about to be built. This allows the extendee (self) to
+                query the dependent's state. Note that *this*
+                package's spec is available as `self.spec`.
+
+        This is useful if there are some common steps to installing
+        all extensions for a certain package.
+
+        """
+        self.setup_environment(spack_env, run_env)
+
+    def setup_dependent_package(self, module, dependent_spec):
+        """Set up Python module-scope variables for dependent packages.
+
+        Called before the install() method of dependents.
+
+        Default implementation does nothing, but this can be
+        overridden by an extendable package to set up the module of
+        its extensions. This is useful if there are some common steps
+        to installing all extensions for a certain package.
+
+        Example :
+
+            1. Extensions often need to invoke the `python`
+               interpreter from the Python installation being
+               extended.  This routine can put a 'python' Executable
+               object in the module scope for the extension package to
+               simplify extension installs.
+
+            2. MPI compilers could set some variables in the
+               dependent's scope that point to `mpicc`, `mpicxx`,
+               etc., allowing them to be called by common names
+               regardless of which MPI is used.
+
+            3. BLAS/LAPACK implementations can set some variables
+               indicating the path to their libraries, since these
+               paths differ by BLAS/LAPACK implementation.
+
+        Args:
+
+            module (module): The Python `module` object of the
+                dependent package. Packages can use this to set
+                module-scope variables for the dependent to use.
+
+            dependent_spec (Spec): The spec of the dependent package
+                about to be built. This allows the extendee (self) to
+                query the dependent's state.  Note that *this*
+                package's spec is available as `self.spec`.
+
+        This is useful if there are some common steps to installing
+        all extensions for a certain package.
+
+        """
+        pass
+
+    def install(self, spec, prefix):
+        """
+        Package implementations override this with their own configuration
+        """
+        raise InstallError("Package %s provides no install method!" %
+                           self.name)
 
     def do_uninstall(self, force=False):
         if not self.installed:
@@ -1036,12 +1190,10 @@ class Package(object):
         # Once everything else is done, run post install hooks
         spack.hooks.post_uninstall(self)
 
-
     def _check_extendable(self):
         if not self.extendable:
             raise ValueError("Package %s is not extendable!" % self.name)
 
-
     def _sanity_check_extension(self):
         if not self.is_extension:
             raise ActivationError("This package is not an extension.")
@@ -1050,12 +1202,13 @@ class Package(object):
         extendee_package._check_extendable()
 
         if not extendee_package.installed:
-            raise ActivationError("Can only (de)activate extensions for installed packages.")
+            raise ActivationError(
+                "Can only (de)activate extensions for installed packages.")
         if not self.installed:
             raise ActivationError("Extensions must first be installed.")
-        if not self.extendee_spec.name in self.extendees:
-            raise ActivationError("%s does not extend %s!" % (self.name, self.extendee.name))
-
+        if self.extendee_spec.name not in self.extendees:
+            raise ActivationError("%s does not extend %s!" %
+                                  (self.name, self.extendee.name))
 
     def do_activate(self, force=False):
         """Called on an etension to invoke the extendee's activate method.
@@ -1065,8 +1218,8 @@ class Package(object):
         """
         self._sanity_check_extension()
 
-        spack.install_layout.check_extension_conflict(
-            self.extendee_spec, self.spec)
+        spack.install_layout.check_extension_conflict(self.extendee_spec,
+                                                      self.spec)
 
         # Activate any package dependencies that are also extensions.
         if not force:
@@ -1078,9 +1231,8 @@ class Package(object):
         self.extendee_spec.package.activate(self, **self.extendee_args)
 
         spack.install_layout.add_extension(self.extendee_spec, self.spec)
-        tty.msg("Activated extension %s for %s"
-                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
-
+        tty.msg("Activated extension %s for %s" %
+                (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
     def activate(self, extension, **kwargs):
         """Symlinks all files from the extension into extendee's install dir.
@@ -1091,6 +1243,7 @@ class Package(object):
         always executed.
 
         """
+
         def ignore(filename):
             return (filename in spack.install_layout.hidden_file_paths or
                     kwargs.get('ignore', lambda f: False)(filename))
@@ -1102,7 +1255,6 @@ class Package(object):
 
         tree.merge(self.prefix, ignore=ignore)
 
-
     def do_deactivate(self, **kwargs):
         """Called on the extension to invoke extendee's deactivate() method."""
         self._sanity_check_extension()
@@ -1120,7 +1272,7 @@ class Package(object):
                 for dep in aspec.traverse():
                     if self.spec == dep:
                         raise ActivationError(
-                            "Cannot deactivate %s beacuse %s is activated and depends on it."
+                            "Cannot deactivate %s because %s is activated and depends on it."  # NOQA: ignore=E501
                             % (self.spec.short_spec, aspec.short_spec))
 
         self.extendee_spec.package.deactivate(self, **self.extendee_args)
@@ -1128,11 +1280,11 @@ class Package(object):
         # redundant activation check -- makes SURE the spec is not
         # still activated even if something was wrong above.
         if self.activated:
-            spack.install_layout.remove_extension(self.extendee_spec, self.spec)
-
-        tty.msg("Deactivated extension %s for %s"
-                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
+            spack.install_layout.remove_extension(self.extendee_spec,
+                                                  self.spec)
 
+        tty.msg("Deactivated extension %s for %s" %
+                (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
     def deactivate(self, extension, **kwargs):
         """Unlinks all files from extension out of this package's install dir.
@@ -1143,6 +1295,7 @@ class Package(object):
         always executed.
 
         """
+
         def ignore(filename):
             return (filename in spack.install_layout.hidden_file_paths or
                     kwargs.get('ignore', lambda f: False)(filename))
@@ -1150,17 +1303,14 @@ class Package(object):
         tree = LinkTree(extension.prefix)
         tree.unmerge(self.prefix, ignore=ignore)
 
-
     def do_restage(self):
         """Reverts expanded/checked out source to a pristine state."""
         self.stage.restage()
 
-
     def do_clean(self):
         """Removes the package's build stage and source tarball."""
         self.stage.destroy()
 
-
     def format_doc(self, **kwargs):
         """Wrap doc string at 72 characters and format nicely"""
         indent = kwargs.get('indent', 0)
@@ -1175,7 +1325,6 @@ class Package(object):
             results.write((" " * indent) + line + "\n")
         return results.getvalue()
 
-
     @property
     def all_urls(self):
         urls = []
@@ -1187,7 +1336,6 @@ class Package(object):
                 urls.append(args['url'])
         return urls
 
-
     def fetch_remote_versions(self):
         """Try to find remote versions of this package using the
            list_url and any other URLs described in the package file."""
@@ -1196,11 +1344,12 @@ class Package(object):
 
         try:
             return spack.util.web.find_versions_of_archive(
-                *self.all_urls, list_url=self.list_url, list_depth=self.list_depth)
+                *self.all_urls,
+                list_url=self.list_url,
+                list_depth=self.list_depth)
         except spack.error.NoNetworkConnectionError as e:
-            tty.die("Package.fetch_versions couldn't connect to:",
-                    e.url, e.message)
-
+            tty.die("Package.fetch_versions couldn't connect to:", e.url,
+                    e.message)
 
     @property
     def rpath(self):
@@ -1212,13 +1361,36 @@ class Package(object):
                       if os.path.isdir(d.prefix.lib64))
         return rpaths
 
-
     @property
     def rpath_args(self):
-        """Get the rpath args as a string, with -Wl,-rpath, for each element."""
+        """
+        Get the rpath args as a string, with -Wl,-rpath, for each element
+        """
         return " ".join("-Wl,-rpath,%s" % p for p in self.rpath)
 
 
+def install_dependency_symlinks(pkg, spec, prefix):
+    """Execute a dummy install and flatten dependencies"""
+    flatten_dependencies(spec, prefix)
+
+
+def flatten_dependencies(spec, flat_dir):
+    """Make each dependency of spec present in dir via symlink."""
+    for dep in spec.traverse(root=False):
+        name = dep.name
+
+        dep_path = spack.install_layout.path_for_spec(dep)
+        dep_files = LinkTree(dep_path)
+
+        os.mkdir(flat_dir + '/' + name)
+
+        conflict = dep_files.find_conflict(flat_dir + '/' + name)
+        if conflict:
+            raise DependencyConflictError(conflict)
+
+        dep_files.merge(flat_dir + '/' + name)
+
+
 def validate_package_url(url_string):
     """Determine whether spack can handle a particular URL or not."""
     url = urlparse(url_string)
@@ -1257,9 +1429,11 @@ def dump_packages(spec, path):
             # Create a source repo and get the pkg directory out of it.
             try:
                 source_repo = spack.repository.Repo(source_repo_root)
-                source_pkg_dir = source_repo.dirname_for_package_name(node.name)
-            except RepoError as e:
-                tty.warn("Warning: Couldn't copy in provenance for %s" % node.name)
+                source_pkg_dir = source_repo.dirname_for_package_name(
+                    node.name)
+            except RepoError:
+                tty.warn("Warning: Couldn't copy in provenance for %s" %
+                         node.name)
 
         # Create a destination repository
         dest_repo_root = join_path(path, node.namespace)
@@ -1279,7 +1453,7 @@ def print_pkg(message):
     """Outputs a message with a package icon."""
     from llnl.util.tty.color import cwrite
     cwrite('@*g{[+]} ')
-    print message
+    print(message)
 
 
 def _hms(seconds):
@@ -1288,41 +1462,53 @@ def _hms(seconds):
     h, m = divmod(m, 60)
 
     parts = []
-    if h: parts.append("%dh" % h)
-    if m: parts.append("%dm" % m)
-    if s: parts.append("%.2fs" % s)
+    if h:
+        parts.append("%dh" % h)
+    if m:
+        parts.append("%dm" % m)
+    if s:
+        parts.append("%.2fs" % s)
     return ' '.join(parts)
 
 
 class FetchError(spack.error.SpackError):
     """Raised when something goes wrong during fetch."""
+
     def __init__(self, message, long_msg=None):
         super(FetchError, self).__init__(message, long_msg)
 
 
 class InstallError(spack.error.SpackError):
     """Raised when something goes wrong during install or uninstall."""
+
     def __init__(self, message, long_msg=None):
         super(InstallError, self).__init__(message, long_msg)
 
 
+class ExternalPackageError(InstallError):
+    """Raised by install() when a package is only for external use."""
+
+
 class PackageStillNeededError(InstallError):
     """Raised when package is still needed by another on uninstall."""
+
     def __init__(self, spec, dependents):
-        super(PackageStillNeededError, self).__init__(
-            "Cannot uninstall %s" % spec)
+        super(PackageStillNeededError, self).__init__("Cannot uninstall %s" %
+                                                      spec)
         self.spec = spec
         self.dependents = dependents
 
 
 class PackageError(spack.error.SpackError):
     """Raised when something is wrong with a package definition."""
+
     def __init__(self, message, long_msg=None):
         super(PackageError, self).__init__(message, long_msg)
 
 
 class PackageVersionError(PackageError):
     """Raised when a version URL cannot automatically be determined."""
+
     def __init__(self, version):
         super(PackageVersionError, self).__init__(
             "Cannot determine a URL automatically for version %s" % version,
@@ -1331,6 +1517,7 @@ class PackageVersionError(PackageError):
 
 class VersionFetchError(PackageError):
     """Raised when a version URL cannot automatically be determined."""
+
     def __init__(self, cls):
         super(VersionFetchError, self).__init__(
             "Cannot fetch versions for package %s " % cls.__name__ +
@@ -1339,12 +1526,15 @@ class VersionFetchError(PackageError):
 
 class NoURLError(PackageError):
     """Raised when someone tries to build a URL for a package with no URLs."""
+
     def __init__(self, cls):
         super(NoURLError, self).__init__(
             "Package %s has no version with a URL." % cls.__name__)
 
 
-class ExtensionError(PackageError): pass
+class ExtensionError(PackageError):
+
+    pass
 
 
 class ExtensionConflictError(ExtensionError):
@@ -1356,3 +1546,12 @@ class ExtensionConflictError(ExtensionError):
 class ActivationError(ExtensionError):
     def __init__(self, msg, long_msg=None):
         super(ActivationError, self).__init__(msg, long_msg)
+
+
+class DependencyConflictError(spack.error.SpackError):
+    """Raised when the dependencies cannot be flattened as asked for."""
+
+    def __init__(self, conflict):
+        super(DependencyConflictError, self).__init__(
+            "%s conflicts with another file in the flattened directory." % (
+                conflict))
diff --git a/lib/spack/spack/package_test.py b/lib/spack/spack/package_test.py
new file mode 100644
index 0000000000..e366b5f0e5
--- /dev/null
+++ b/lib/spack/spack/package_test.py
@@ -0,0 +1,66 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+def compile_c_and_execute(source_file, include_flags, link_flags):
+    """Compile C @p source_file with @p include_flags and @p link_flags,
+    run and return the output.
+    """
+    cc = which('cc')
+    flags = include_flags
+    flags.extend([source_file])
+    cc('-c', *flags)
+    name = os.path.splitext(os.path.basename(source_file))[0]
+    cc('-o', "check", "%s.o" % name,
+       *link_flags)
+
+    check = Executable('./check')
+    return check(return_output=True)
+
+
+def compare_output(current_output, blessed_output):
+    """Compare blessed and current output of executables."""
+    if not (current_output == blessed_output):
+        print "Produced output does not match expected output."
+        print "Expected output:"
+        print '-' * 80
+        print blessed_output
+        print '-' * 80
+        print "Produced output:"
+        print '-' * 80
+        print current_output
+        print '-' * 80
+        raise RuntimeError("Ouput check failed.",
+                           "See spack_output.log for details")
+
+
+def compare_output_file(current_output, blessed_output_file):
+    """Same as above, but when the blessed output is given as a file."""
+    with open(blessed_output_file, 'r') as f:
+        blessed_output = f.read()
+
+    compare_output(current_output, blessed_output)
diff --git a/lib/spack/spack/parse.py b/lib/spack/spack/parse.py
index e9467aa685..8adf957e7f 100644
--- a/lib/spack/spack/parse.py
+++ b/lib/spack/spack/parse.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
 import itertools
diff --git a/lib/spack/spack/patch.py b/lib/spack/spack/patch.py
index b82a047753..c2e181be2f 100644
--- a/lib/spack/spack/patch.py
+++ b/lib/spack/spack/patch.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index 9d219a1a6e..4820584150 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -1,33 +1,33 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://scalability-llnl.github.io/spack
+# For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 import spack
 from spack.version import *
 
 class PreferredPackages(object):
-    _default_order = {'compiler' : [ 'gcc', 'intel', 'clang', 'pgi', 'xlc' ] }, # Arbitrary, but consistent
+    _default_order = {'compiler' : [ 'gcc', 'intel', 'clang', 'pgi', 'xlc' ] } # Arbitrary, but consistent
 
     def __init__(self):
         self.preferred = spack.config.get_config('packages')
diff --git a/lib/spack/spack/repository.py b/lib/spack/spack/repository.py
index 3c3ba08bcc..70134964ad 100644
--- a/lib/spack/spack/repository.py
+++ b/lib/spack/spack/repository.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://software.llnl.gov/spack
+# For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import exceptions
@@ -316,6 +316,11 @@ class RepoPath(object):
         return self.repo_for_pkg(spec).get(spec)
 
 
+    def get_pkg_class(self, pkg_name):
+        """Find a class for the spec's package and return the class object."""
+        return self.repo_for_pkg(pkg_name).get_pkg_class(pkg_name)
+
+
     @_autospec
     def dump_provenance(self, spec, path):
         """Dump provenance information for a spec to a particular path.
@@ -550,7 +555,7 @@ class Repo(object):
 
         key = hash(spec)
         if new or key not in self._instances:
-            package_class = self._get_pkg_class(spec.name)
+            package_class = self.get_pkg_class(spec.name)
             try:
                 copy = spec.copy() # defensive copy.  Package owns its spec.
                 self._instances[key] = package_class(copy)
@@ -715,7 +720,7 @@ class Repo(object):
         return self._modules[pkg_name]
 
 
-    def _get_pkg_class(self, pkg_name):
+    def get_pkg_class(self, pkg_name):
         """Get the class for the package out of its module.
 
         First loads (or fetches from cache) a module for the
diff --git a/lib/spack/spack/resource.py b/lib/spack/spack/resource.py
index ddfaaf4cb0..24b675f8da 100644
--- a/lib/spack/spack/resource.py
+++ b/lib/spack/spack/resource.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://software.llnl.gov/spack
+# For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Describes an optional resource needed for a build.
 
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index eee9318550..f71d56435e 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -1,22 +1,22 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
 # You should have received a copy of the GNU Lesser General Public License
 # along with this program; if not, write to the Free Software Foundation,
@@ -72,7 +72,9 @@ Here is the EBNF grammar for a spec::
   dep_list     = { ^ spec }
   spec         = id [ options ]
   options      = { @version-list | +variant | -variant | ~variant |
-                   %compiler | =architecture }
+                   %compiler | arch=architecture | [ flag ]=value}
+  flag         = { cflags | cxxflags | fcflags | fflags | cppflags |
+                   ldflags | ldlibs }
   variant      = id
   architecture = id
   compiler     = id [ version-list ]
@@ -80,6 +82,9 @@ Here is the EBNF grammar for a spec::
   version      = id | id: | :id | id:id
   id           = [A-Za-z0-9_][A-Za-z0-9_.-]*
 
+Identifiers using the <name>=<value> command, such as architectures and
+compiler flags, require a space before the name.
+
 There is one context-sensitive part: ids in versions may contain '.', while
 other ids may not.
 
@@ -90,9 +95,7 @@ thing.  Spack uses ~variant in directory names and in the canonical form of
 specs to avoid ambiguity.  Both are provided because ~ can cause shell
 expansion when it is the first character in an id typed on the command line.
 """
-from collections import namedtuple
 import sys
-import imp
 import itertools
 import hashlib
 import base64
@@ -102,7 +105,6 @@ import yaml
 from yaml.error import MarkedYAMLError
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path
 from llnl.util.lang import *
 from llnl.util.tty.color import *
 
@@ -110,10 +112,11 @@ import spack
 import spack.architecture
 import spack.parse
 import spack.error
-#import spack.compilers as compilers
+import spack.compilers as compilers
 
+# TODO: move display_specs to some other location.
+from spack.cmd.find import display_specs
 from spack.version import *
-from spack.util.naming import mod_to_class
 from spack.util.string import *
 from spack.util.prefix import Prefix
 from spack.virtual import ProviderIndex
@@ -124,7 +127,7 @@ identifier_re = r'\w[\w-]*'
 # Convenient names for color formats so that other things can use them
 compiler_color         = '@g'
 version_color          = '@c'
-architecture_color           = '@m'
+architecture_color     = '@m'
 enabled_variant_color  = '@B'
 disabled_variant_color = '@r'
 dependency_color       = '@.'
@@ -148,7 +151,6 @@ _separators = '[%s]' % ''.join(color_formats.keys())
    every time we call str()"""
 _any_version = VersionList([':'])
 
-
 def index_specs(specs):
     """Take a list of specs and return a dict of lists.  Dict is
        keyed by spec name and lists include all specs with the
@@ -301,22 +303,25 @@ class VariantSpec(object):
        on the particular package being built, and each named variant can
        be enabled or disabled.
     """
-    def __init__(self, name, enabled):
+    def __init__(self, name, value):
         self.name = name
-        self.enabled = enabled
+        self.value = value
 
 
     def _cmp_key(self):
-        return (self.name, self.enabled)
+        return (self.name, self.value)
 
 
     def copy(self):
-        return VariantSpec(self.name, self.enabled)
+        return VariantSpec(self.name, self.value)
 
 
     def __str__(self):
-        out = '+' if self.enabled else '~'
-        return out + self.name
+        if self.value in [True,False]:
+            out = '+' if self.value else '~'
+            return out + self.name
+        else:
+            return ' ' + self.name + "=" + self.value
 
 
 class VariantMap(HashableMap):
@@ -327,10 +332,10 @@ class VariantMap(HashableMap):
 
     def satisfies(self, other, strict=False):
         if strict or self.spec._concrete:
-            return all(k in self and self[k].enabled == other[k].enabled
+            return all(k in self and self[k].value == other[k].value
                        for k in other)
         else:
-            return all(self[k].enabled == other[k].enabled
+            return all(self[k].value == other[k].value
                        for k in other if k in self)
 
 
@@ -348,7 +353,7 @@ class VariantMap(HashableMap):
         changed = False
         for k in other:
             if k in self:
-                if self[k].enabled != other[k].enabled:
+                if self[k].value != other[k].value:
                     raise UnsatisfiableVariantSpecError(self[k], other[k])
             else:
                 self[k] = other[k].copy()
@@ -358,7 +363,7 @@ class VariantMap(HashableMap):
     @property
     def concrete(self):
         return self.spec._concrete or all(
-            v in self for v in self.spec.package.variants)
+            v in self for v in self.spec.package_class.variants)
 
 
     def copy(self):
@@ -373,6 +378,70 @@ class VariantMap(HashableMap):
         return ''.join(str(self[key]) for key in sorted_keys)
 
 
+_valid_compiler_flags = [
+    'cflags', 'cxxflags', 'fflags', 'ldflags', 'ldlibs', 'cppflags']
+
+class FlagMap(HashableMap):
+    def __init__(self, spec):
+        super(FlagMap, self).__init__()
+        self.spec = spec
+
+
+    def satisfies(self, other, strict=False):
+        if strict or (self.spec and self.spec._concrete):
+            return all(f in self and set(self[f]) <= set(other[f])
+                       for f in other)
+        else:
+            return all(set(self[f]) <= set(other[f])
+                   for f in other if (other[f] != [] and f in self))
+
+
+    def constrain(self, other):
+        """Add all flags in other that aren't in self to self.
+
+        Return whether the spec changed.
+        """
+        if other.spec and other.spec._concrete:
+            for k in self:
+                if k not in other:
+                    raise UnsatisfiableCompilerFlagSpecError(self[k], '<absent>')
+
+        changed = False
+        for k in other:
+            if k in self and not set(self[k]) <= set(other[k]):
+                raise UnsatisfiableCompilerFlagSpecError(
+                    ' '.join(f for f in self[k]), ' '.join( f for f in other[k]))
+            elif k not in self:
+                self[k] = other[k]
+                changed = True
+        return changed
+
+    @staticmethod
+    def valid_compiler_flags():
+        return _valid_compiler_flags
+
+    @property
+    def concrete(self):
+        return all(flag in self for flag in _valid_compiler_flags)
+
+
+    def copy(self):
+        clone = FlagMap(None)
+        for name, value in self.items():
+            clone[name] = value
+        return clone
+
+
+    def _cmp_key(self):
+        return ''.join(str(key) + ' '.join(str(v) for v in value) for key, value in sorted(self.items()))
+
+
+    def __str__(self):
+        sorted_keys = filter(lambda flag: self[flag] != [], sorted(self.keys()))
+        cond_symbol = ' ' if len(sorted_keys)>0 else ''
+        return cond_symbol + ' '.join(str(key) + '=\"' + ' '.join(str(f) for f in self[key]) + '\"' for key in sorted_keys)
+
+
 class DependencyMap(HashableMap):
     """Each spec has a DependencyMap containing specs for its dependencies.
        The DependencyMap is keyed by name. """
@@ -414,10 +483,13 @@ class Spec(object):
         self.versions = other.versions
         self.architecture = other.architecture
         self.compiler = other.compiler
+        self.compiler_flags = other.compiler_flags
+        self.compiler_flags.spec = self
         self.dependencies = other.dependencies
         self.variants = other.variants
         self.variants.spec = self
         self.namespace = other.namespace
+        self._hash = other._hash
 
         # Specs are by default not assumed to be normal, but in some
         # cases we've read them from a file want to assume normal.
@@ -425,8 +497,14 @@ class Spec(object):
         # package.py files for.
         self._normal = kwargs.get('normal', False)
         self._concrete = kwargs.get('concrete', False)
+#ifdef NEW
+
+        # Allow a spec to be constructed with an external path.
+        self.external  = kwargs.get('external', None)
+#else /* not NEW */
         self.external = None
         self.external_module = None
+#endif /* not NEW */
 
         # This allows users to construct a spec DAG with literals.
         # Note that given two specs a and b, Spec(a) copies a, but
@@ -444,12 +522,29 @@ class Spec(object):
         self.versions.add(version)
 
 
-    def _add_variant(self, name, enabled):
+    def _add_variant(self, name, value):
         """Called by the parser to add a variant."""
         if name in self.variants: raise DuplicateVariantError(
                 "Cannot specify variant '%s' twice" % name)
-        self.variants[name] = VariantSpec(name, enabled)
+        if isinstance(value, basestring) and value.upper() == 'TRUE':
+            value = True
+        elif isinstance(value, basestring) and value.upper() == 'FALSE':
+            value = False
+        self.variants[name] = VariantSpec(name, value)
+
 
+    def _add_flag(self, name, value):
+        """Called by the parser to add a known flag.
+        Known flags currently include "arch"
+        """
+        valid_flags = FlagMap.valid_compiler_flags()
+        if name == 'arch':
+            self._set_architecture(value)
+        elif name in valid_flags:
+            assert(self.compiler_flags is not None)
+            self.compiler_flags[name] = value.split()
+        else:
+            self._add_variant(name,value)
 
     def _set_compiler(self, compiler):
         """Called by the parser to set the compiler."""
@@ -461,18 +556,8 @@ class Spec(object):
     def _set_architecture(self, architecture):
         """Called by the parser to set the architecture."""
         if self.architecture: raise DuplicateArchitectureError(
-                "Spec for '%s' cannot have two architectures." % self.name)  
-        if '-' in architecture:
-            os, target = architecture.split('-')
-
-        elif architecture in ['frontend','backend','fe','be']:
-            os = architecture
-            target = architecture
-        else:
-            os = None
-            target = architecture
-
-        self.architecture = spack.architecture.Arch(os, target)
+                "Spec for '%s' cannot have two architectures." % self.name)
+        self.architecture = architecture
 
 
     def _add_dependency(self, spec):
@@ -487,7 +572,7 @@ class Spec(object):
     #
     @property
     def fullname(self):
-        return '%s.%s' % (self.namespace, self.name) if self.namespace else self.name
+        return '%s.%s' % (self.namespace, self.name) if self.namespace else (self.name if self.name else '')
 
 
     @property
@@ -515,6 +600,14 @@ class Spec(object):
 
 
     @property
+    def package_class(self):
+        """Internal package call gets only the class object for a package.
+           Use this to just get package metadata.
+        """
+        return spack.repo.get_pkg_class(self.name)
+
+
+    @property
     def virtual(self):
         """Right now, a spec is virtual if no package exists with its name.
 
@@ -529,7 +622,7 @@ class Spec(object):
     @staticmethod
     def is_virtual(name):
         """Test if a name is virtual without requiring a Spec."""
-        return not spack.repo.exists(name)
+        return (not name is None) and ( not spack.repo.exists(name) )
 
 
     @property
@@ -548,8 +641,8 @@ class Spec(object):
                               and self.architecture
                               and self.architecture.concrete
                               and self.compiler and self.compiler.concrete
+                              and self.compiler_flags.concrete
                               and self.dependencies.concrete)
-
         return self._concrete
 
 
@@ -671,16 +764,23 @@ class Spec(object):
         """
         Return a hash of the entire spec DAG, including connectivity.
         """
-        yaml_text = yaml.dump(
-            self.to_node_dict(), default_flow_style=True, width=sys.maxint)
-        sha = hashlib.sha1(yaml_text)
-        return base64.b32encode(sha.digest()).lower()[:length]
-
+        if self._hash:
+            return self._hash[:length]
+        else:
+            yaml_text = yaml.dump(
+                self.to_node_dict(), default_flow_style=True, width=sys.maxint)
+            sha = hashlib.sha1(yaml_text)
+            b32_hash = base64.b32encode(sha.digest()).lower()[:length]
+            if self.concrete:
+                self._hash = b32_hash
+            return b32_hash
 
     def to_node_dict(self):
+        params = dict( (name, v.value) for name, v in self.variants.items() )
+        params.update( dict( (name, value) for name, value in self.compiler_flags.items()) )
         d = {
-            'variants' : dict(
-                (name,v.enabled) for name, v in self.variants.items()),
+            'parameters' : params,
+            'arch' : self.architecture,
             'dependencies' : dict((d, self.dependencies[d].dag_hash())
                                   for d in sorted(self.dependencies))
         }
@@ -702,6 +802,7 @@ class Spec(object):
         else:
             d['compiler'] = None
         d.update(self.versions.to_dict())
+
         return { self.name : d }
 
 
@@ -723,16 +824,35 @@ class Spec(object):
         spec = Spec(name)
         spec.namespace = node.get('namespace', None)
         spec.versions = VersionList.from_dict(node)
+#ifdef NEW
+        spec.architecture = node['arch']
+
+        if 'hash' in node:
+            spec._hash = node['hash']
+
+#else /* not NEW */
         # TODO: Need to fix the architecture.Target.from_dict
         spec.architecture = spack.architecture.arch_from_dict(node['architecture'])
 
+#endif /* not NEW */
         if node['compiler'] is None:
             spec.compiler = None
         else:
             spec.compiler = CompilerSpec.from_dict(node)
 
-        for name, enabled in node['variants'].items():
-            spec.variants[name] = VariantSpec(name, enabled)
+        if 'parameters' in node:
+            for name, value in node['parameters'].items():
+                if name in _valid_compiler_flags:
+                    spec.compiler_flags[name] = value
+                else:
+                    spec.variants[name] = VariantSpec(name, value)
+        elif 'variants' in node:
+            for name, value in node['variants'].items():
+                spec.variants[name] = VariantSpec(name, value)
+            for name in FlagMap.valid_compiler_flags():
+                spec.compiler_flags[name] = []
+        else:
+            raise SpackRecordError("Did not find a valid format for variants in YAML file")
 
         return spec
 
@@ -794,11 +914,13 @@ class Spec(object):
             # Concretize virtual dependencies last.  Because they're added
             # to presets below, their constraints will all be merged, but we'll
             # still need to select a concrete package later.
-            changed |= any(
-                (spack.concretizer.concretize_architecture(self),
-                 spack.concretizer.concretize_compiler(self),
-                 spack.concretizer.concretize_version(self),
-                 spack.concretizer.concretize_variants(self)))
+            if not self.virtual:
+                changed |= any(
+                    (spack.concretizer.concretize_architecture(self),
+                     spack.concretizer.concretize_compiler(self),
+                     spack.concretizer.concretize_compiler_flags(self),#has to be concretized after compiler
+                     spack.concretizer.concretize_version(self),
+                     spack.concretizer.concretize_variants(self)))
             presets[self.name] = self
 
         visited.add(self.name)
@@ -809,11 +931,32 @@ class Spec(object):
         """Replace this virtual spec with a concrete spec."""
         assert(self.virtual)
         for name, dependent in self.dependents.items():
-            if not dependent.external:
-                del dependent.dependencies[self.name]
+            # remove self from all dependents.
+            del dependent.dependencies[self.name]
+
+            # add the replacement, unless it is already a dep of dependent.
+            if concrete.name not in dependent.dependencies:
                 dependent._add_dependency(concrete)
 
 
+    def _replace_node(self, replacement):
+        """Replace this spec with another.
+
+        Connects all dependents of this spec to its replacement, and
+        disconnects this spec from any dependencies it has. New spec
+        will have any dependencies the replacement had, and may need
+        to be normalized.
+
+        """
+        for name, dependent in self.dependents.items():
+            del dependent.dependencies[self.name]
+            dependent._add_dependency(replacement)
+
+        for name, dep in self.dependencies.items():
+            del dep.dependents[self.name]
+            del self.dependencies[dep.name]
+
+
     def _expand_virtual_packages(self):
         """Find virtual packages in this spec, replace them with providers,
            and normalize again to include the provider's (potentially virtual)
@@ -831,18 +974,80 @@ class Spec(object):
               this are infrequent, but should implement this before it is
               a problem.
         """
+        # Make an index of stuff this spec already provides
+        self_index = ProviderIndex(self.traverse(), restrict=True)
+
         changed = False
         done = False
         while not done:
             done = True
             for spec in list(self.traverse()):
-                if spack.concretizer.concretize_virtual_and_external(spec):
-                    done = False
+                replacement = None
+                if spec.virtual:
+                    replacement = self._find_provider(spec, self_index)
+                    if replacement:
+                        # TODO: may break if in-place on self but
+                        # shouldn't happen if root is traversed first.
+                        spec._replace_with(replacement)
+                        done=False
+                        break
+
+                if not replacement:
+                    # Get a list of possible replacements in order of preference.
+                    candidates = spack.concretizer.choose_virtual_or_external(spec)
+
+                    # Try the replacements in order, skipping any that cause
+                    # satisfiability problems.
+                    for replacement in candidates:
+                        if replacement is spec:
+                            break
+
+                        # Replace spec with the candidate and normalize
+                        copy = self.copy()
+                        copy[spec.name]._dup(replacement.copy(deps=False))
+
+                        try:
+                            # If there are duplicate providers or duplicate provider
+                            # deps, consolidate them and merge constraints.
+                            copy.normalize(force=True)
+                            break
+                        except SpecError as e:
+                            # On error, we'll try the next replacement.
+                            continue
+
+                # If replacement is external then trim the dependencies
+                if replacement.external:
+                    if (spec.dependencies):
+                        changed = True
+                        spec.dependencies = DependencyMap()
+                    replacement.dependencies = DependencyMap()
+
+                # TODO: could this and the stuff in _dup be cleaned up?
+                def feq(cfield, sfield):
+                    return (not cfield) or (cfield == sfield)
+
+                if replacement is spec or (feq(replacement.name, spec.name) and
+                    feq(replacement.versions, spec.versions) and
+                    feq(replacement.compiler, spec.compiler) and
+                    feq(replacement.architecture, spec.architecture) and
+                    feq(replacement.dependencies, spec.dependencies) and
+                    feq(replacement.variants, spec.variants) and
+                    feq(replacement.external, spec.external)):
+                    continue
+
+                # Refine this spec to the candidate. This uses
+                # replace_with AND dup so that it can work in
+                # place. TODO: make this more efficient.
+                if spec.virtual:
+                    spec._replace_with(replacement)
                     changed = True
+                if spec._dup(replacement, deps=False, cleardeps=False):
+                    changed = True
+
+                self_index.update(spec)
+                done=False
+                break
 
-        # If there are duplicate providers or duplicate provider deps, this
-        # consolidates them and merge constraints.
-        changed |= self.normalize(force=True)
         return changed
 
 
@@ -858,6 +1063,8 @@ class Spec(object):
            with requirements of its pacakges.  See flatten() and normalize() for
            more details on this.
         """
+        if not self.name:
+            raise SpecError("Attempting to concretize anonymous spec")
 
         if self._concrete:
             return
@@ -866,7 +1073,7 @@ class Spec(object):
         force = False
 
         while changed:
-            changes = (self.normalize(force=force),
+            changes = (self.normalize(force),
                        self._expand_virtual_packages(),
                        self._concretize_helper())
             changed = any(changes)
@@ -992,8 +1199,8 @@ class Spec(object):
 
     def _find_provider(self, vdep, provider_index):
         """Find provider for a virtual spec in the provider index.
-        Raise an exception if there is a conflicting virtual
-        dependency already in this spec.
+           Raise an exception if there is a conflicting virtual
+           dependency already in this spec.
         """
         assert(vdep.virtual)
         providers = provider_index.providers_for(vdep)
@@ -1001,6 +1208,11 @@ class Spec(object):
         # If there is a provider for the vpkg, then use that instead of
         # the virtual package.
         if providers:
+            # Remove duplicate providers that can concretize to the same result.
+            for provider in providers:
+                for spec in providers:
+                    if spec is not provider and provider.satisfies(spec):
+                        providers.remove(spec)
             # Can't have multiple providers for the same thing in one spec.
             if len(providers) > 1:
                 raise MultipleProviderError(vdep, providers)
@@ -1034,17 +1246,14 @@ class Spec(object):
         """
         changed = False
 
-        # If it's a virtual dependency, try to find a provider and
-        # merge that.
+        # If it's a virtual dependency, try to find an existing
+        # provider in the spec, and merge that.
         if dep.virtual:
             visited.add(dep.name)
             provider = self._find_provider(dep, provider_index)
             if provider:
                 dep = provider
-
         else:
-            # if it's a real dependency, check whether it provides
-            # something already required in the spec.
             index = ProviderIndex([dep], restrict=True)
             for vspec in (v for v in spec_deps.values() if v.virtual):
                 if index.providers_for(vspec):
@@ -1056,13 +1265,11 @@ class Spec(object):
                     if required:
                         raise UnsatisfiableProviderSpecError(required[0], dep)
             provider_index.update(dep)
-
         # If the spec isn't already in the set of dependencies, clone
         # it from the package description.
         if dep.name not in spec_deps:
             spec_deps[dep.name] = dep.copy()
             changed = True
-
         # Constrain package information with spec info
         try:
             changed |= spec_deps[dep.name].constrain(dep)
@@ -1105,7 +1312,6 @@ class Spec(object):
             for dep_name in pkg.dependencies:
                 # Do we depend on dep_name?  If so pkg_dep is not None.
                 pkg_dep = self._evaluate_dependency_conditions(dep_name)
-
                 # If pkg_dep is a dependency, merge it.
                 if pkg_dep:
                     changed |= self._merge_dependency(
@@ -1130,8 +1336,10 @@ class Spec(object):
 
            TODO: normalize should probably implement some form of cycle detection,
            to ensure that the spec is actually a DAG.
-
         """
+        if not self.name:
+            raise SpecError("Attempting to normalize anonymous spec")
+
         if self._normal and not force:
             return False
 
@@ -1141,13 +1349,14 @@ class Spec(object):
         # Get all the dependencies into one DependencyMap
         spec_deps = self.flat_dependencies(copy=False)
 
-        # Initialize index of virtual dependency providers
-        index = ProviderIndex(spec_deps.values(), restrict=True)
+        # Initialize index of virtual dependency providers if
+        # concretize didn't pass us one already
+        provider_index = ProviderIndex(spec_deps.values(), restrict=True)
 
         # traverse the package DAG and fill out dependencies according
         # to package files & their 'when' specs
         visited = set()
-        any_change = self._normalize_helper(visited, spec_deps, index)
+        any_change = self._normalize_helper(visited, spec_deps, provider_index)
 
         # If there are deps specified but not visited, they're not
         # actually deps of this package.  Raise an error.
@@ -1175,17 +1384,17 @@ class Spec(object):
         """
         for spec in self.traverse():
             # Don't get a package for a virtual name.
-            if not spec.virtual:
+            if (not spec.virtual) and spec.name:
                 spack.repo.get(spec.fullname)
 
             # validate compiler in addition to the package name.
-#            if spec.compiler:
-#                if not compilers.supported(spec.compiler):
-#                    raise UnsupportedCompilerError(spec.compiler.name)
+            if spec.compiler:
+                if not compilers.supported(spec.compiler):
+                    raise UnsupportedCompilerError(spec.compiler.name)
 
             # Ensure that variants all exist.
             for vname, variant in spec.variants.items():
-                if vname not in spec.package.variants:
+                if vname not in spec.package_class.variants:
                     raise UnknownVariantError(spec.name, vname)
 
 
@@ -1196,7 +1405,7 @@ class Spec(object):
         """
         other = self._autospec(other)
 
-        if not self.name == other.name:
+        if not (self.name == other.name or (not self.name) or (not other.name) ):
             raise UnsatisfiableSpecNameError(self.name, other.name)
 
         if other.namespace is not None:
@@ -1208,14 +1417,14 @@ class Spec(object):
 
         for v in other.variants:
             if (v in self.variants and
-                self.variants[v].enabled != other.variants[v].enabled):
+                self.variants[v].value != other.variants[v].value):
                 raise UnsatisfiableVariantSpecError(self.variants[v],
                                                     other.variants[v])
 
         # TODO: Check out the logic here
         if self.architecture is not None and other.architecture is not None:
             if self.architecture != other.architecture:
-                raise UnsatisfiableTargetSpecError(self.architecture,
+                raise UnsatisfiableArchitectureSpecError(self.architecture,
                                                          other.architecture)
 
         changed = False
@@ -1228,6 +1437,8 @@ class Spec(object):
         changed |= self.versions.intersect(other.versions)
         changed |= self.variants.constrain(other.variants)
 
+        changed |= self.compiler_flags.constrain(other.compiler_flags)
+
         old = self.architecture
         self.architecture = self.architecture or other.architecture
         changed |= (self.architecture != old)
@@ -1298,27 +1509,18 @@ class Spec(object):
             return spec_like
 
         try:
-            return spack.spec.Spec(spec_like)
+            spec = spack.spec.Spec(spec_like)
+            if not spec.name:
+                raise SpecError("anonymous package -- this will always be handled")
+            return spec
         except SpecError:
             return parse_anonymous_spec(spec_like, self.name)
 
-    #def add_target_from_string(self, target):
-    #    if target is None:
-    #        self.architecture.target = self.architecture.platform.target('default_target')
-    #    else:
-    #        self.architecture.target = self.architecture.platform.target(target)
-
-    #def add_operating_system_from_string(self, os):
-    #    if os is None:
-    #        self.architecture.platform_os = self.architecture.platform.operating_system('default_os')
-    #    else:
-    #        self.architecture.platform_os = self.architecture.platform.operating_system(os)
-
 
     def satisfies(self, other, deps=True, strict=False):
-        """determine if this spec satisfies all constraints of another.
+        """Determine if this spec satisfies all constraints of another.
 
-        there are two senses for satisfies:
+        There are two senses for satisfies:
 
           * `loose` (default): the absence of a constraint in self
             implies that it *could* be satisfied by other, so we only
@@ -1340,8 +1542,8 @@ class Spec(object):
                             return True
             return False
 
-        # otherwise, first thing we care about is whether the name matches
-        if self.name != other.name:
+        # Otherwise, first thing we care about is whether the name matches
+        if self.name != other.name and self.name and other.name:
             return False
 
         # namespaces either match, or other doesn't require one.
@@ -1355,18 +1557,20 @@ class Spec(object):
         elif strict and (self.versions or other.versions):
             return False
 
-        # none indicates no constraints when not strict.
+        # None indicates no constraints when not strict.
         if self.compiler and other.compiler:
             if not self.compiler.satisfies(other.compiler, strict=strict):
-                return  False
+                return False
         elif strict and (other.compiler and not self.compiler):
             return False
 
-        if not self.variants.satisfies(other.variants, strict=strict):
+        var_strict = strict
+        if (not self.name) or (not other.name):
+            var_strict = True
+        if not self.variants.satisfies(other.variants, strict=var_strict):
             return False
 
-
-        # Target satisfaction is currently just class equality.
+        # Architecture satisfaction is currently just string equality.
         # If not strict, None means unconstrained.
         if isinstance(self.architecture, basestring):
             self.add_architecture_from_string(self.architecture)
@@ -1380,9 +1584,15 @@ class Spec(object):
         elif strict and (other.architecture and not self.architecture):
             return False
 
+        if not self.compiler_flags.satisfies(other.compiler_flags, strict=strict):
+            return False
+
         # If we need to descend into dependencies, do it, otherwise we're done.
         if deps:
-            return self.satisfies_dependencies(other, strict=strict)
+            deps_strict = strict
+            if not (self.name and other.name):
+                deps_strict=True
+            return self.satisfies_dependencies(other, strict=deps_strict)
         else:
             return True
 
@@ -1446,8 +1656,6 @@ class Spec(object):
                Whether deps should be copied too.  Set to False to copy a
                spec but not its dependencies.
         """
-
-        # TODO: Check if comparisons for tuple are valid
         # We don't count dependencies as changes here
         changed = True
         if hasattr(self, 'name'):
@@ -1465,11 +1673,16 @@ class Spec(object):
         if kwargs.get('cleardeps', True):
             self.dependents = DependencyMap()
             self.dependencies = DependencyMap()
+        self.compiler_flags = other.compiler_flags.copy()
         self.variants = other.variants.copy()
         self.variants.spec = self
         self.external = other.external
         self.namespace = other.namespace
+#ifdef NEW
+        self._hash = other._hash
+#else /* not NEW */
         self.external_module = other.external_module
+#endif /* not NEW */
 
         # If we copy dependencies, preserve DAG structure in the new spec
         if kwargs.get('deps', True):
@@ -1595,7 +1808,9 @@ class Spec(object):
                 self.versions,
                 self.variants,
                 self.architecture,
-                self.compiler)
+                self.compiler,
+                self.compiler_flags,
+                self.dag_hash())
 
 
     def eq_node(self, other):
@@ -1624,7 +1839,7 @@ class Spec(object):
         return colorize_spec(self)
 
 
-    def format(self, format_string='$_$@$%@$+$=', **kwargs):
+    def format(self, format_string='$_$@$%@+$+$=', **kwargs):
         """Prints out particular pieces of a spec, depending on what is
            in the format string.  The format strings you can provide are::
 
@@ -1633,8 +1848,10 @@ class Spec(object):
                $@   Version with '@' prefix
                $%   Compiler with '%' prefix
                $%@  Compiler with '%' prefix & compiler version with '@' prefix
+               $%+  Compiler with '%' prefix & compiler flags prefixed by name
+               $%@+ Compiler, compiler version, and compiler flags with same prefixes as above
                $+   Options
-               $=   Architecture with '=' prefix
+               $=   Architecture prefixed by 'arch='
                $#   7-char prefix of DAG hash with '-' prefix
                $$   $
 
@@ -1645,8 +1862,9 @@ class Spec(object):
                ${COMPILER}      Full compiler string
                ${COMPILERNAME}  Compiler name
                ${COMPILERVER}   Compiler version
+               ${COMPILERFLAGS} Compiler flags
                ${OPTIONS}       Options
-               ${TARGET}        Target
+               ${ARCHITECTURE}  Architecture
                ${SHA1}          Dependencies 8-char sha1 prefix
 
                ${SPACK_ROOT}    The spack root directory
@@ -1691,7 +1909,8 @@ class Spec(object):
                 fmt += 's'
 
                 if c == '_':
-                    out.write(fmt % self.name)
+                    name = self.name if self.name else ''
+                    out.write(fmt % name)
                 elif c == '.':
                     out.write(fmt % self.fullname)
                 elif c == '@':
@@ -1704,10 +1923,9 @@ class Spec(object):
                 elif c == '+':
                     if self.variants:
                         write(fmt % str(self.variants), c)
-                # TODO: Check string methods here
                 elif c == '=':
                     if self.architecture:
-                        write(fmt % (c + str(self.architecture)), c)
+                        write(fmt % (' arch' + c + str(self.architecture)), c)
                 elif c == '#':
                     out.write('-' + fmt % (self.dag_hash(7)))
                 elif c == '$':
@@ -1724,11 +1942,16 @@ class Spec(object):
                     if (self.compiler and self.compiler.versions and
                         self.compiler.versions != _any_version):
                         write(c + str(self.compiler.versions), '%')
+                elif c == '+':
+                    if self.compiler_flags:
+                        write(fmt % str(self.compiler_flags), '%')
+                    compiler = False
                 elif c == '$':
                     escape = True
+                    compiler = False
                 else:
                     out.write(c)
-                compiler = False
+                    compiler = False
 
             elif named:
                 if not c == '}':
@@ -1738,6 +1961,7 @@ class Spec(object):
                     named_str += c
                     continue;
                 if named_str == 'PACKAGE':
+                    name = self.name if self.name else ''
                     write(fmt % self.name, '@')
                 if named_str == 'VERSION':
                     if self.versions and self.versions != _any_version:
@@ -1751,12 +1975,15 @@ class Spec(object):
                 elif named_str == 'COMPILERVER':
                     if self.compiler:
                         write(fmt % self.compiler.versions, '%')
+                elif named_str == 'COMPILERFLAGS':
+                    if self.compiler:
+                        write(fmt % str(self.compiler_flags), '%')
                 elif named_str == 'OPTIONS':
                     if self.variants:
                         write(fmt % str(self.variants), '+')
                 elif named_str == 'ARCHITECTURE':
                     if self.architecture:
-                        write(fmt % self.architecture, '=')
+                        write(fmt % str(self.architecture), '=')
                 elif named_str == 'SHA1':
                     if self.dependencies:
                         out.write(fmt % str(self.dag_hash(7)))
@@ -1829,7 +2056,7 @@ class Spec(object):
         showid = kwargs.pop('ids',   False)
         cover  = kwargs.pop('cover', 'nodes')
         indent = kwargs.pop('indent', 0)
-        fmt    = kwargs.pop('format', '$_$@$%@$+$=')
+        fmt    = kwargs.pop('format', '$_$@$%@+$+$=')
         prefix = kwargs.pop('prefix', None)
         check_kwargs(kwargs, self.tree)
 
@@ -1861,12 +2088,13 @@ class Spec(object):
 #
 # These are possible token types in the spec grammar.
 #
-DEP, AT, COLON, COMMA, ON, OFF, PCT, EQ, ID = range(9)
+HASH, DEP, AT, COLON, COMMA, ON, OFF, PCT, EQ, QT, ID = range(11)
 
 class SpecLexer(spack.parse.Lexer):
     """Parses tokens that make up spack specs."""
     def __init__(self):
         super(SpecLexer, self).__init__([
+            (r'/',         lambda scanner, val: self.token(HASH,  val)),
             (r'\^',        lambda scanner, val: self.token(DEP,   val)),
             (r'\@',        lambda scanner, val: self.token(AT,    val)),
             (r'\:',        lambda scanner, val: self.token(COLON, val)),
@@ -1878,6 +2106,7 @@ class SpecLexer(spack.parse.Lexer):
             (r'\=',        lambda scanner, val: self.token(EQ,    val)),
             # This is more liberal than identifier_re (see above).
             # Checked by check_identifier() for better error messages.
+            (r'([\"\'])(?:(?=(\\?))\2.)*?\1',lambda scanner, val: self.token(QT, val)),
             (r'\w[\w.-]*', lambda scanner, val: self.token(ID,    val)),
             (r'\s+',       lambda scanner, val: None)])
 
@@ -1885,26 +2114,51 @@ class SpecLexer(spack.parse.Lexer):
 class SpecParser(spack.parse.Parser):
     def __init__(self):
         super(SpecParser, self).__init__(SpecLexer())
-
+        self.previous = None
 
     def do_parse(self):
         specs = []
         try:
             while self.next:
+                # TODO: clean this parsing up a bit
+                if self.previous:
+                    specs.append(self.spec(self.previous.value))
                 if self.accept(ID):
-                    specs.append(self.spec())
+                    self.previous = self.token
+                    if self.accept(EQ):
+                        if not specs:
+                            specs.append(self.spec(None))
+                        if self.accept(QT):
+                            self.token.value = self.token.value[1:-1]
+                        else:
+                            self.expect(ID)
+                        specs[-1]._add_flag(self.previous.value, self.token.value)
+                    else:
+                        specs.append(self.spec(self.previous.value))
+                    self.previous = None
+                elif self.accept(HASH):
+                    specs.append(self.spec_by_hash())
 
                 elif self.accept(DEP):
                     if not specs:
-                        self.last_token_error("Dependency has no package")
-                    self.expect(ID)
-                    specs[-1]._add_dependency(self.spec())
+                        self.previous = self.token
+                        specs.append(self.spec(None))
+                        self.previous = None
+                    if self.accept(HASH):
+                        specs[-1]._add_dependency(self.spec_by_hash())
+                    else:
+                        self.expect(ID)
+                        specs[-1]._add_dependency(self.spec(self.token.value))
 
                 else:
-                    self.unexpected_token()
+                    # Attempt to construct an anonymous spec, but check that the first token is valid
+                    # TODO: Is this check even necessary, or will it all be Lex errors now?
+                    specs.append(self.spec(None,True))
+
         except spack.parse.ParseError, e:
             raise SpecParseError(e)
 
+
         return specs
 
 
@@ -1913,15 +2167,35 @@ class SpecParser(spack.parse.Parser):
         return self.compiler()
 
 
-    def spec(self):
+    def spec_by_hash(self):
+        self.expect(ID)
+
+        specs = spack.installed_db.query()
+        matches = [spec for spec in specs if
+                   spec.dag_hash()[:len(self.token.value)] == self.token.value]
+
+        if not matches:
+            tty.die("%s does not match any installed packages." %self.token.value)
+
+        if len(matches) != 1:
+            raise AmbiguousHashError("Multiple packages specify hash %s." % self.token.value, *matches)
+
+        return matches[0]
+
+
+    def spec(self, name, check_valid_token = False):
         """Parse a spec out of the input.  If a spec is supplied, then initialize
            and return it instead of creating a new one."""
-
-        spec_namespace, dot, spec_name = self.token.value.rpartition('.')
-        if not spec_namespace:
+        if name:
+            spec_namespace, dot, spec_name = name.rpartition('.')
+            if not spec_namespace:
+                spec_namespace = None
+            self.check_identifier(spec_name)
+        else:
             spec_namespace = None
+            spec_name = None
+
 
-        self.check_identifier(spec_name)
 
         # This will init the spec without calling __init__.
         spec = Spec.__new__(Spec)
@@ -1931,10 +2205,15 @@ class SpecParser(spack.parse.Parser):
         spec.architecture = None
         spec.compiler = None
         spec.external = None
+#ifdef NEW
+        spec.compiler_flags = FlagMap(spec)
+#else /* not NEW */
         spec.external_module = None
+#endif /* not NEW */
         spec.dependents   = DependencyMap()
         spec.dependencies = DependencyMap()
         spec.namespace = spec_namespace
+        spec._hash = None
 
         spec._normal = False
         spec._concrete = False
@@ -1943,26 +2222,50 @@ class SpecParser(spack.parse.Parser):
         # unspecified or not.
         added_version = False
 
+        if self.previous and self.previous.value == DEP:
+            if self.accept(HASH):
+                spec.add_dependency(self.spec_by_hash())
+            else:
+                self.expect(ID)
+                if self.accept(EQ):
+                    raise SpecParseError(spack.parse.ParseError("","","Expected dependency received anonymous spec"))
+                spec.add_dependency(self.spec(self.token.value))
+
         while self.next:
             if self.accept(AT):
                 vlist = self.version_list()
                 for version in vlist:
                     spec._add_version(version)
                 added_version = True
+                check_valid_token = False
 
             elif self.accept(ON):
                 spec._add_variant(self.variant(), True)
+                check_valid_token = False
 
             elif self.accept(OFF):
-                spec._add_variant(self.variant(), False)
+                spec._add_variant(self.variant(),False)
+                check_valid_token = False
 
             elif self.accept(PCT):
                 spec._set_compiler(self.compiler())
+                check_valid_token = False
 
-            elif self.accept(EQ):
-                spec._set_architecture(self.architecture())
+            elif self.accept(ID):
+                self.previous = self.token
+                if self.accept(EQ):
+                    if self.accept(QT):
+                        self.token.value = self.token.value[1:-1]
+                    else:
+                        self.expect(ID)
+                    spec._add_flag(self.previous.value, self.token.value)
+                    self.previous = None
+                else:
+                    return spec
 
             else:
+                if check_valid_token:
+                    self.unexpected_token()
                 break
 
         # If there was no version in the spec, consier it an open range
@@ -1972,13 +2275,17 @@ class SpecParser(spack.parse.Parser):
         return spec
 
 
-    def variant(self):
-        self.expect(ID)
-        self.check_identifier()
-        return self.token.value
-
+    def variant(self,name=None):
+        #TODO: Make generalized variants possible
+        if name:
+            return name
+        else:
+            self.expect(ID)
+            self.check_identifier()
+            return self.token.value
 
     def architecture(self):
+        #TODO: Make this work properly as a subcase of variant (includes adding names to grammar)
         self.expect(ID)
         return self.token.value
 
@@ -2060,8 +2367,10 @@ def parse_anonymous_spec(spec_like, pkg_name):
     if isinstance(spec_like, str):
         try:
             anon_spec = Spec(spec_like)
+            if anon_spec.name != pkg_name:
+                raise SpecParseError(spack.parse.ParseError("","","Expected anonymous spec for package %s but found spec for package %s" % (pkg_name, anon_spec.name) ))
         except SpecParseError:
-            anon_spec = Spec(pkg_name + spec_like)
+            anon_spec = Spec(pkg_name + ' ' +  spec_like)
             if anon_spec.name != pkg_name: raise ValueError(
                     "Invalid spec for package %s: %s" % (pkg_name, spec_like))
     else:
@@ -2128,7 +2437,7 @@ class UnknownArchitectureSpecError(SpecError):
                                             architecture_spec_entry))
 
 class DuplicateArchitectureError(SpecError):
-    """Raised when the same target occurs in a spec twice."""
+    """Raised when the same architecture occurs in a spec twice."""
     def __init__(self, message):
         super(DuplicateArchitectureError, self).__init__(message)
 
@@ -2169,7 +2478,6 @@ class MultipleProviderError(SpecError):
         self.vpkg = vpkg
         self.providers = providers
 
-
 class UnsatisfiableSpecError(SpecError):
     """Raised when a spec conflicts with package constraints.
        Provide the requirement that was violated when raising."""
@@ -2208,12 +2516,17 @@ class UnsatisfiableVariantSpecError(UnsatisfiableSpecError):
         super(UnsatisfiableVariantSpecError, self).__init__(
             provided, required, "variant")
 
+class UnsatisfiableCompilerFlagSpecError(UnsatisfiableSpecError):
+    """Raised when a spec variant conflicts with package constraints."""
+    def __init__(self, provided, required):
+        super(UnsatisfiableCompilerFlagSpecError, self).__init__(
+            provided, required, "compiler_flags")
 
-class UnsatisfiableTargetSpecError(UnsatisfiableSpecError):
-    """Raised when a spec target conflicts with package constraints."""
+class UnsatisfiableArchitectureSpecError(UnsatisfiableSpecError):
+    """Raised when a spec architecture conflicts with package constraints."""
     def __init__(self, provided, required):
-        super(UnsatisfiableTargetSpecError, self).__init__(
-            provided, required, "target")
+        super(UnsatisfiableArchitectureSpecError, self).__init__(
+            provided, required, "architecture")
 
 
 class UnsatisfiableProviderSpecError(UnsatisfiableSpecError):
@@ -2234,3 +2547,13 @@ class UnsatisfiableDependencySpecError(UnsatisfiableSpecError):
 class SpackYAMLError(spack.error.SpackError):
     def __init__(self, msg, yaml_error):
         super(SpackYAMLError, self).__init__(msg, str(yaml_error))
+
+class SpackRecordError(spack.error.SpackError):
+    def __init__(self, msg):
+        super(SpackRecordError, self).__init__(msg)
+
+class AmbiguousHashError(SpecError):
+    def __init__(self, msg, *specs):
+        super(AmbiguousHashError, self).__init__(msg)
+        for spec in specs:
+            print '    ', spec.format('$.$@$%@+$+$=$#')
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index f88f82fc2d..a76ec168ad 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import errno
@@ -89,7 +89,7 @@ class Stage(object):
     """
 
     def __init__(self, url_or_fetch_strategy,
-                 name=None, mirror_path=None, keep=False):
+                 name=None, mirror_path=None, keep=False, path=None):
         """Create a stage object.
            Parameters:
              url_or_fetch_strategy
@@ -135,7 +135,10 @@ class Stage(object):
 
         # Try to construct here a temporary name for the stage directory
         # If this is a named stage, then construct a named path.
-        self.path = join_path(spack.stage_path, self.name)
+        if path is not None:
+            self.path = path
+        else:
+            self.path = join_path(spack.stage_path, self.name)
 
         # Flag to decide whether to delete the stage folder on exit or not
         self.keep = keep
@@ -208,6 +211,18 @@ class Stage(object):
         return False
 
     @property
+    def expected_archive_files(self):
+        """Possible archive file paths."""
+        paths = []
+        if isinstance(self.fetcher, fs.URLFetchStrategy):
+            paths.append(os.path.join(self.path, os.path.basename(self.fetcher.url)))
+
+        if self.mirror_path:
+            paths.append(os.path.join(self.path, os.path.basename(self.mirror_path)))
+
+        return paths
+
+    @property
     def archive_file(self):
         """Path to the source archive within this stage directory."""
         paths = []
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index e851b123ed..cac7c2f058 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -1,39 +1,47 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
-import unittest
-import nose
 
-from spack.test.tally_plugin import Tally
-from llnl.util.filesystem import join_path
 import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
-
+import nose
 import spack
-
+from llnl.util.filesystem import join_path
+from llnl.util.tty.colify import colify
+from spack.test.tally_plugin import Tally
 """Names of tests to be included in Spack's test suite"""
+#ifdef NEW
+test_names = ['versions', 'url_parse', 'url_substitution', 'packages', 'stage',
+              'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize',
+              'multimethod', 'install', 'package_sanity', 'config',
+              'directory_layout', 'pattern', 'python_version', 'git_fetch',
+              'svn_fetch', 'hg_fetch', 'mirror', 'modules', 'url_extrapolate',
+              'cc', 'link_tree', 'spec_yaml', 'optional_deps',
+              'make_executable', 'configure_guess', 'lock', 'database',
+              'namespace_trie', 'yaml', 'sbang', 'environment',
+              'cmd.uninstall', 'cmd.test_install']
+#else /* not NEW */
 test_names = ['architecture',
               'versions',
               'url_parse',
@@ -68,6 +76,7 @@ test_names = ['architecture',
               'namespace_trie',
               'yaml',
               'sbang']
+#endif /* not NEW */
 
 
 def list_tests():
@@ -78,8 +87,6 @@ def list_tests():
 def run(names, outputDir, verbose=False):
     """Run tests with the supplied names.  Names should be a list.  If
        it's empty, run ALL of Spack's tests."""
-    verbosity = 1 if not verbose else 2
-
     if not names:
         names = test_names
     else:
@@ -93,7 +100,7 @@ def run(names, outputDir, verbose=False):
     tally = Tally()
     for test in names:
         module = 'spack.test.' + test
-        print module
+        print(module)
 
         tty.msg("Running test: %s" % test)
 
@@ -103,15 +110,13 @@ def run(names, outputDir, verbose=False):
             xmlOutputFname = "unittests-{0}.xml".format(test)
             xmlOutputPath = join_path(outputDir, xmlOutputFname)
             runOpts += ["--with-xunit",
-                "--xunit-file={0}".format(xmlOutputPath)]
+                        "--xunit-file={0}".format(xmlOutputPath)]
         argv = [""] + runOpts + [module]
-        result = nose.run(argv=argv, addplugins=[tally])
+        nose.run(argv=argv, addplugins=[tally])
 
     succeeded = not tally.failCount and not tally.errorCount
-    tty.msg("Tests Complete.",
-            "%5d tests run" % tally.numberOfTestsRun,
-            "%5d failures" % tally.failCount,
-            "%5d errors" % tally.errorCount)
+    tty.msg("Tests Complete.", "%5d tests run" % tally.numberOfTestsRun,
+            "%5d failures" % tally.failCount, "%5d errors" % tally.errorCount)
 
     if succeeded:
         tty.info("OK", format='g')
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index f3f6d4a22e..ea2b164462 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This test checks that the Spack cc compiler wrapper is parsing
@@ -28,6 +28,8 @@ arguments correctly.
 """
 import os
 import unittest
+import tempfile
+import shutil
 
 from llnl.util.filesystem import *
 import spack
@@ -54,20 +56,66 @@ class CompilerTest(unittest.TestCase):
         self.cc = Executable(join_path(spack.build_env_path, "cc"))
         self.ld = Executable(join_path(spack.build_env_path, "ld"))
         self.cpp = Executable(join_path(spack.build_env_path, "cpp"))
+        self.cxx = Executable(join_path(spack.build_env_path, "c++"))
+        self.fc = Executable(join_path(spack.build_env_path, "fc"))
 
-        os.environ['SPACK_CC'] = "/bin/mycc"
-        os.environ['SPACK_PREFIX'] = "/usr"
+        self.realcc = "/bin/mycc"
+        self.prefix = "/spack-test-prefix"
+
+        os.environ['SPACK_CC'] = self.realcc
+        os.environ['SPACK_CXX'] = self.realcc
+        os.environ['SPACK_FC'] = self.realcc
+
+        os.environ['SPACK_PREFIX'] = self.prefix
         os.environ['SPACK_ENV_PATH']="test"
         os.environ['SPACK_DEBUG_LOG_DIR'] = "."
         os.environ['SPACK_COMPILER_SPEC'] = "gcc@4.4.7"
         os.environ['SPACK_SHORT_SPEC'] = "foo@1.2"
 
+        os.environ['SPACK_CC_RPATH_ARG']  = "-Wl,-rpath,"
+        os.environ['SPACK_CXX_RPATH_ARG'] = "-Wl,-rpath,"
+        os.environ['SPACK_F77_RPATH_ARG'] = "-Wl,-rpath,"
+        os.environ['SPACK_FC_RPATH_ARG']  = "-Wl,-rpath,"
+
+        # Make some fake dependencies
+        self.tmp_deps = tempfile.mkdtemp()
+        self.dep1 = join_path(self.tmp_deps, 'dep1')
+        self.dep2 = join_path(self.tmp_deps, 'dep2')
+        self.dep3 = join_path(self.tmp_deps, 'dep3')
+        self.dep4 = join_path(self.tmp_deps, 'dep4')
+
+        mkdirp(join_path(self.dep1, 'include'))
+        mkdirp(join_path(self.dep1, 'lib'))
+
+        mkdirp(join_path(self.dep2, 'lib64'))
+
+        mkdirp(join_path(self.dep3, 'include'))
+        mkdirp(join_path(self.dep3, 'lib64'))
+
+        mkdirp(join_path(self.dep4, 'include'))
+
+        if 'SPACK_DEPENDENCIES' in os.environ:
+            del os.environ['SPACK_DEPENDENCIES']
+
+
+    def tearDown(self):
+        shutil.rmtree(self.tmp_deps, True)
+
 
     def check_cc(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
         self.assertEqual(self.cc(*args, output=str).strip(), expected)
 
 
+    def check_cxx(self, command, args, expected):
+        os.environ['SPACK_TEST_COMMAND'] = command
+        self.assertEqual(self.cxx(*args, output=str).strip(), expected)
+
+    def check_fc(self, command, args, expected):
+        os.environ['SPACK_TEST_COMMAND'] = command
+        self.assertEqual(self.fc(*args, output=str).strip(), expected)
+
+
     def check_ld(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
         self.assertEqual(self.ld(*args, output=str).strip(), expected)
@@ -92,6 +140,10 @@ class CompilerTest(unittest.TestCase):
         self.check_cpp('dump-mode', [], "cpp")
 
 
+    def test_as_mode(self):
+        self.check_cc('dump-mode', ['-S'], "as")
+
+
     def test_ccld_mode(self):
         self.check_cc('dump-mode', [], "ccld")
         self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld")
@@ -104,27 +156,167 @@ class CompilerTest(unittest.TestCase):
         self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld")
 
 
-    def test_includes(self):
-        self.check_cc('dump-includes', test_command,
-                      "\n".join(["/test/include", "/other/include"]))
+    def test_flags(self):
+        os.environ['SPACK_LDFLAGS'] = '-L foo'
+        os.environ['SPACK_LDLIBS'] = '-lfoo'
+        os.environ['SPACK_CPPFLAGS'] = '-g -O1'
+        os.environ['SPACK_CFLAGS'] = '-Wall'
+        os.environ['SPACK_CXXFLAGS'] = '-Werror'
+        os.environ['SPACK_FFLAGS'] = '-w'
+
+        # Test ldflags added properly in ld mode
+        self.check_ld('dump-args', test_command,
+                      "ld " +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
+                      '-L foo ' +
+                      ' '.join(test_command) + ' ' +
+                      '-lfoo')
+
+        # Test cppflags added properly in cpp mode
+        self.check_cpp('dump-args', test_command,
+                       "cpp " +
+                      '-g -O1 ' +
+                      ' '.join(test_command))
+
+        # Test ldflags, cppflags, and language specific flags are added in proper order
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-g -O1 ' +
+                      '-Wall ' +
+                      '-L foo ' +
+                      ' '.join(test_command) + ' ' +
+                      '-lfoo')
+
+        self.check_cxx('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-g -O1 ' +
+                      '-Werror ' +
+                      '-L foo ' +
+                      ' '.join(test_command) + ' ' +
+                      '-lfoo')
+
+        self.check_fc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-w ' +
+                      '-g -O1 ' +
+                      '-L foo ' +
+                      ' '.join(test_command) + ' ' +
+                      '-lfoo')
+
+        os.environ['SPACK_LDFLAGS']=''
+        os.environ['SPACK_LDLIBS']=''
+
+
+    def test_dep_rpath(self):
+        """Ensure RPATHs for root package are added."""
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      ' '.join(test_command))
+
+
+    def test_dep_include(self):
+        """Ensure a single dependency include directory is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep4
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-I' + self.dep4 + '/include ' +
+                      ' '.join(test_command))
+
+
+    def test_dep_lib(self):
+        """Ensure a single dependency RPATH is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+                      ' '.join(test_command))
+
+
+    def test_all_deps(self):
+        """Ensure includes and RPATHs for all deps are added. """
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+
+        # This is probably more constrained than it needs to be; it
+        # checks order within prepended args and doesn't strictly have
+        # to.  We could loosen that if it becomes necessary
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+
+                      '-I' + self.dep4 + '/include ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep3 + '/lib64 ' +
+                      '-I' + self.dep3 + '/include ' +
+
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+
+                      '-L' + self.dep1 + '/lib ' +
+                      '-Wl,-rpath,' + self.dep1 + '/lib ' +
+                      '-I' + self.dep1 + '/include ' +
+
+                      ' '.join(test_command))
+
+
+    def test_ld_deps(self):
+        """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+
+        self.check_ld('dump-args', test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-rpath ' + self.dep3 + '/lib64 ' +
 
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-rpath ' + self.dep2 + '/lib64 ' +
 
-    def test_libraries(self):
-        self.check_cc('dump-libraries', test_command,
-                      "\n".join(["/test/lib", "/other/lib"]))
+                      '-L' + self.dep1 + '/lib ' +
+                      '-rpath ' + self.dep1 + '/lib ' +
 
+                      ' '.join(test_command))
 
-    def test_libs(self):
-        self.check_cc('dump-libs', test_command,
-                      "\n".join(["lib1", "lib2", "lib3", "lib4"]))
+    def test_ld_deps_reentrant(self):
+        """Make sure ld -r is handled correctly on OS's where it doesn't
+           support rpaths."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([self.dep1])
 
+        os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=linux-x86_64"
+        reentrant_test_command = ['-r'] + test_command
+        self.check_ld('dump-args', reentrant_test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
 
-    def test_rpaths(self):
-        self.check_cc('dump-rpaths', test_command,
-                      "\n".join(["/first/rpath", "/second/rpath", "/third/rpath", "/fourth/rpath"]))
+                      '-L' + self.dep1 + '/lib ' +
+                      '-rpath ' + self.dep1 + '/lib ' +
 
+                      '-r ' +
+                      ' '.join(test_command))
 
-    def test_other_args(self):
-        self.check_cc('dump-other-args', test_command,
-                      "\n".join(["arg1", "-Wl,--start-group", "arg2", "arg3", "arg4",
-                                 "-Wl,--end-group", "arg5", "arg6"]))
+        os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=darwin-x86_64"
+        self.check_ld('dump-args', reentrant_test_command,
+                      'ld ' +
+                      '-L' + self.dep1 + '/lib ' +
+                      '-r ' +
+                      ' '.join(test_command))
diff --git a/lib/spack/spack/test/cmd/__init__.py b/lib/spack/spack/test/cmd/__init__.py
new file mode 100644
index 0000000000..ed1ec23bca
--- /dev/null
+++ b/lib/spack/spack/test/cmd/__init__.py
@@ -0,0 +1,24 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
diff --git a/lib/spack/spack/test/cmd/test_install.py b/lib/spack/spack/test/cmd/test_install.py
new file mode 100644
index 0000000000..d17e013ed2
--- /dev/null
+++ b/lib/spack/spack/test/cmd/test_install.py
@@ -0,0 +1,190 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import collections
+from contextlib import contextmanager
+
+import StringIO
+
+FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
+
+# Monkey-patch open to write module files to a StringIO instance
+@contextmanager
+def mock_open(filename, mode):
+    if not mode == 'wb':
+        raise RuntimeError('test.test_install : unexpected opening mode for monkey-patched open')
+
+    FILE_REGISTRY[filename] = StringIO.StringIO()
+
+    try:
+        yield FILE_REGISTRY[filename]
+    finally:
+        handle = FILE_REGISTRY[filename]
+        FILE_REGISTRY[filename] = handle.getvalue()
+        handle.close()
+
+import os
+import itertools
+import unittest
+
+import spack
+import spack.cmd
+
+
+# The use of __import__ is necessary to maintain a name with hyphen (which cannot be an identifier in python)
+test_install = __import__("spack.cmd.test-install", fromlist=['test_install'])
+
+
+class MockSpec(object):
+    def __init__(self, name, version, hashStr=None):
+        self.dependencies = {}
+        self.name = name
+        self.version = version
+        self.hash = hashStr if hashStr else hash((name, version))
+
+    def traverse(self, order=None):
+        for _, spec in self.dependencies.items():
+            yield spec
+        yield self
+        #allDeps = itertools.chain.from_iterable(i.traverse() for i in self.dependencies.itervalues())
+        #return set(itertools.chain([self], allDeps))
+
+    def dag_hash(self):
+        return self.hash
+
+    @property
+    def short_spec(self):
+        return '-'.join([self.name, str(self.version), str(self.hash)])
+
+
+class MockPackage(object):
+    def __init__(self, spec, buildLogPath):
+        self.name = spec.name
+        self.spec = spec
+        self.installed = False
+        self.build_log_path = buildLogPath
+
+    def do_install(self, *args, **kwargs):
+        self.installed = True
+
+
+class MockPackageDb(object):
+    def __init__(self, init=None):
+        self.specToPkg = {}
+        if init:
+            self.specToPkg.update(init)
+
+    def get(self, spec):
+        return self.specToPkg[spec]
+
+
+def mock_fetch_log(path):
+    return []
+
+specX = MockSpec('X', "1.2.0")
+specY = MockSpec('Y', "2.3.8")
+specX.dependencies['Y'] = specY
+pkgX = MockPackage(specX, 'logX')
+pkgY = MockPackage(specY, 'logY')
+
+
+class MockArgs(object):
+    def __init__(self, package):
+        self.package = package
+        self.jobs = None
+        self.no_checksum = False
+        self.output = None
+
+
+# TODO: add test(s) where Y fails to install
+class TestInstallTest(unittest.TestCase):
+    """
+    Tests test-install where X->Y
+    """
+
+    def setUp(self):
+        super(TestInstallTest, self).setUp()
+
+        # Monkey patch parse specs
+        def monkey_parse_specs(x, concretize):
+            if x == 'X':
+                return [specX]
+            elif x == 'Y':
+                return [specY]
+            return []
+
+        self.parse_specs = spack.cmd.parse_specs
+        spack.cmd.parse_specs = monkey_parse_specs
+
+        # Monkey patch os.mkdirp
+        self.os_mkdir = os.mkdir
+        os.mkdir = lambda x: True
+
+        # Monkey patch open
+        test_install.open = mock_open
+
+        # Clean FILE_REGISTRY
+        FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
+
+        pkgX.installed = False
+        pkgY.installed = False
+
+        # Monkey patch pkgDb
+        self.saved_db = spack.repo
+        pkgDb = MockPackageDb({specX: pkgX, specY: pkgY})
+        spack.repo = pkgDb
+
+    def tearDown(self):
+        # Remove the monkey patched test_install.open
+        test_install.open = open
+
+        # Remove the monkey patched os.mkdir
+        os.mkdir = self.os_mkdir
+        del self.os_mkdir
+
+        # Remove the monkey patched parse_specs
+        spack.cmd.parse_specs = self.parse_specs
+        del self.parse_specs
+        super(TestInstallTest, self).tearDown()
+
+        spack.repo = self.saved_db
+
+    def test_installing_both(self):
+        test_install.test_install(None, MockArgs('X') )
+        self.assertEqual(len(FILE_REGISTRY), 1)
+        for _, content in FILE_REGISTRY.items():
+            self.assertTrue('tests="2"' in content)
+            self.assertTrue('failures="0"' in content)
+            self.assertTrue('errors="0"' in content)
+
+    def test_dependency_already_installed(self):
+        pkgX.installed = True
+        pkgY.installed = True
+        test_install.test_install(None, MockArgs('X'))
+        self.assertEqual(len(FILE_REGISTRY), 1)
+        for _, content in FILE_REGISTRY.items():
+            self.assertTrue('tests="2"' in content)
+            self.assertTrue('failures="0"' in content)
+            self.assertTrue('errors="0"' in content)
+            self.assertEqual(sum('skipped' in line for line in content.split('\n')), 2)
diff --git a/lib/spack/spack/test/cmd/uninstall.py b/lib/spack/spack/test/cmd/uninstall.py
new file mode 100644
index 0000000000..9fffaace40
--- /dev/null
+++ b/lib/spack/spack/test/cmd/uninstall.py
@@ -0,0 +1,61 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import spack.test.mock_database
+
+from spack.cmd.uninstall import uninstall
+
+
+class MockArgs(object):
+    def __init__(self, packages, all=False, force=False, dependents=False):
+        self.packages = packages
+        self.all = all
+        self.force = force
+        self.dependents = dependents
+        self.yes_to_all = True
+
+
+class TestUninstall(spack.test.mock_database.MockDatabase):
+    def test_uninstall(self):
+        parser = None
+        # Multiple matches
+        args = MockArgs(['mpileaks'])
+        self.assertRaises(SystemExit, uninstall, parser, args)
+        # Installed dependents
+        args = MockArgs(['libelf'])
+        self.assertRaises(SystemExit, uninstall, parser, args)
+        # Recursive uninstall
+        args = MockArgs(['callpath'], all=True, dependents=True)
+        uninstall(parser, args)
+
+        all_specs = spack.install_layout.all_specs()
+        self.assertEqual(len(all_specs), 7)
+        # query specs with multiple configurations
+        mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')]
+        callpath_specs = [s for s in all_specs if s.satisfies('callpath')]
+        mpi_specs = [s for s in all_specs if s.satisfies('mpi')]
+
+        self.assertEqual(len(mpileaks_specs), 0)
+        self.assertEqual(len(callpath_specs), 0)
+        self.assertEqual(len(mpi_specs),      3)
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 3fb8417c3e..49281b9a0c 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -1,29 +1,30 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack
 from spack.spec import Spec, CompilerSpec
+from spack.version import ver
 from spack.concretize import find_spec
 from spack.test.mock_packages_test import *
 
@@ -37,11 +38,20 @@ class ConcretizeTest(MockPackagesTest):
             for name in abstract.variants:
                 avariant = abstract.variants[name]
                 cvariant = concrete.variants[name]
-                self.assertEqual(avariant.enabled, cvariant.enabled)
+                self.assertEqual(avariant.value, cvariant.value)
+
+        if abstract.compiler_flags:
+            for flag in abstract.compiler_flags:
+                aflag = abstract.compiler_flags[flag]
+                cflag = concrete.compiler_flags[flag]
+                self.assertTrue(set(aflag) <= set(cflag))
 
         for name in abstract.package.variants:
             self.assertTrue(name in concrete.variants)
 
+        for flag in concrete.compiler_flags.valid_compiler_flags():
+            self.assertTrue(flag in concrete.compiler_flags)
+
         if abstract.compiler and abstract.compiler.concrete:
             self.assertEqual(abstract.compiler, concrete.compiler)
 
@@ -74,9 +84,22 @@ class ConcretizeTest(MockPackagesTest):
     def test_concretize_variant(self):
         self.check_concretize('mpich+debug')
         self.check_concretize('mpich~debug')
+        self.check_concretize('mpich debug=2')
         self.check_concretize('mpich')
 
 
+    def test_conretize_compiler_flags(self):
+        self.check_concretize('mpich cppflags="-O3"')
+
+
+    def test_concretize_preferred_version(self):
+        spec = self.check_concretize('python')
+        self.assertEqual(spec.versions, ver('2.7.11'))
+
+        spec = self.check_concretize('python@3.5.1')
+        self.assertEqual(spec.versions, ver('3.5.1'))
+
+
     def test_concretize_with_virtual(self):
         self.check_concretize('mpileaks ^mpi')
         self.check_concretize('mpileaks ^mpi@:1.1')
@@ -142,6 +165,34 @@ class ConcretizeTest(MockPackagesTest):
                                 for spec in spack.repo.providers_for('mpi@3')))
 
 
+    def test_concretize_two_virtuals(self):
+        """Test a package with multiple virtual dependencies."""
+        s = Spec('hypre').concretize()
+
+
+    def test_concretize_two_virtuals_with_one_bound(self):
+        """Test a package with multiple virtual dependencies and one preset."""
+        s = Spec('hypre ^openblas').concretize()
+
+
+    def test_concretize_two_virtuals_with_two_bound(self):
+        """Test a package with multiple virtual dependencies and two of them preset."""
+        s = Spec('hypre ^openblas ^netlib-lapack').concretize()
+
+
+    def test_concretize_two_virtuals_with_dual_provider(self):
+        """Test a package with multiple virtual dependencies and force a provider
+           that provides both."""
+        s = Spec('hypre ^openblas-with-lapack').concretize()
+
+
+    def test_concretize_two_virtuals_with_dual_provider_and_a_conflict(self):
+        """Test a package with multiple virtual dependencies and force a provider
+           that provides both, and another conflicting package that provides one."""
+        s = Spec('hypre ^openblas-with-lapack ^netlib-lapack')
+        self.assertRaises(spack.spec.MultipleProviderError, s.concretize)
+
+
     def test_virtual_is_fully_expanded_for_callpath(self):
         # force dependence on fake "zmpi" by asking for MPI 10.0
         spec = Spec('callpath ^mpi@10.0')
@@ -194,7 +245,7 @@ class ConcretizeTest(MockPackagesTest):
 
 
     def test_external_package(self):
-        spec = Spec('externaltool')
+        spec = Spec('externaltool%gcc')
         spec.concretize()
 
         self.assertEqual(spec['externaltool'].external, '/path/to/external_tool')
@@ -282,3 +333,9 @@ class ConcretizeTest(MockPackagesTest):
                  Spec('e'))
         self.assertEqual(None, find_spec(s['b'], lambda s: '+foo' in s))
 
+
+    def test_compiler_child(self):
+        s = Spec('mpileaks%clang ^dyninst%gcc')
+        s.concretize()
+        self.assertTrue(s['mpileaks'].satisfies('%clang'))
+        self.assertTrue(s['dyninst'].satisfies('%gcc'))
diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py
index daa4c572bd..7d71cc1c7f 100644
--- a/lib/spack/spack/test/config.py
+++ b/lib/spack/spack/test/config.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import shutil
@@ -120,6 +120,10 @@ b_comps = {
         }
 }
 
+# Some Sample repo data
+repos_low = [ "/some/path" ]
+repos_high = [ "/some/other/path" ]
+
 class ConfigTest(MockPackagesTest):
 
     def setUp(self):
@@ -138,6 +142,19 @@ class ConfigTest(MockPackagesTest):
         """Check that named compilers in comps match Spack's config."""
         config = spack.config.get_config('compilers')
         compiler_list = ['cc', 'cxx', 'f77', 'fc']
+#ifdef NEW
+        for key in compiler_names:
+            for c in compiler_list:
+                expected = comps[arch][key][c]
+                actual = config[arch][key][c]
+                self.assertEqual(expected, actual)
+
+    def test_write_list_in_memory(self):
+        spack.config.update_config('repos', repos_low, 'test_low_priority')
+        spack.config.update_config('repos', repos_high, 'test_high_priority')
+        config = spack.config.get_config('repos')
+        self.assertEqual(config, repos_high+repos_low)
+#else /* not NEW */
         param_list = ['modules', 'paths', 'spec', 'operating_system']
         for alias, compiler in config.items():
             if compiler['spec'] in compiler_names:
@@ -149,6 +166,7 @@ class ConfigTest(MockPackagesTest):
                     expected = comps[alias]['paths'][c]
                     actual = config[alias]['paths'][c]
                     self.assertEqual(expected, actual)
+#endif /* not NEW */
 
     def test_write_key_in_memory(self):
         # Write b_comps "on top of" a_comps.
@@ -169,5 +187,22 @@ class ConfigTest(MockPackagesTest):
         spack.config.clear_config_caches()
 
         # Same check again, to ensure consistency.
+#ifdef NEW
+        self.check_config(a_comps, 'x86_64_E5v2_IntelIB', 'gcc@4.7.3', 'gcc@4.5.0')
+        self.check_config(b_comps, 'x86_64_E5v3', 'icc@10.0', 'icc@11.1', 'clang@3.3')
+
+    def test_write_to_same_priority_file(self):
+        # Write b_comps in the same file as a_comps.
+        spack.config.update_config('compilers', a_comps, 'test_low_priority')
+        spack.config.update_config('compilers', b_comps, 'test_low_priority')
+
+        # Clear caches so we're forced to read from disk.
+        spack.config.clear_config_caches()
+
+        # Same check again, to ensure consistency.
+        self.check_config(a_comps, 'x86_64_E5v2_IntelIB', 'gcc@4.7.3', 'gcc@4.5.0')
+        self.check_config(b_comps, 'x86_64_E5v3', 'icc@10.0', 'icc@11.1', 'clang@3.3')
+#else /* not NEW */
         self.check_config(a_comps, 'gcc@4.7.3', 'gcc@4.5.0')
         self.check_config(b_comps, 'icc@10.0', 'icc@11.1', 'clang@3.3')
+#endif /* not NEW */
diff --git a/lib/spack/spack/test/configure_guess.py b/lib/spack/spack/test/configure_guess.py
index 2440d120e5..bad3673e7a 100644
--- a/lib/spack/spack/test/configure_guess.py
+++ b/lib/spack/spack/test/configure_guess.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import shutil
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index 9a57e1f03e..e1322f2081 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -1,42 +1,39 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 These tests check the database is functioning properly,
 both in memory and in its file
 """
+import os.path
 import multiprocessing
-import shutil
-import tempfile
 
 import spack
 from llnl.util.filesystem import join_path
 from llnl.util.lock import *
 from llnl.util.tty.colify import colify
-from spack.database import Database
-from spack.directory_layout import YamlDirectoryLayout
-from spack.test.mock_packages_test import *
+from spack.test.mock_database import MockDatabase
 
 
 def _print_ref_counts():
@@ -74,80 +71,7 @@ def _print_ref_counts():
     colify(recs, cols=3)
 
 
-class DatabaseTest(MockPackagesTest):
-
-    def _mock_install(self, spec):
-        s = Spec(spec)
-        s.concretize()
-        pkg = spack.repo.get(s)
-        pkg.do_install(fake=True)
-
-
-    def _mock_remove(self, spec):
-        specs = spack.installed_db.query(spec)
-        assert(len(specs) == 1)
-        spec = specs[0]
-        spec.package.do_uninstall(spec)
-
-
-    def setUp(self):
-        super(DatabaseTest, self).setUp()
-        #
-        # TODO: make the mockup below easier.
-        #
-
-        # Make a fake install directory
-        self.install_path = tempfile.mkdtemp()
-        self.spack_install_path = spack.install_path
-        spack.install_path = self.install_path
-
-        self.install_layout = YamlDirectoryLayout(self.install_path)
-        self.spack_install_layout = spack.install_layout
-        spack.install_layout = self.install_layout
-
-        # Make fake database and fake install directory.
-        self.installed_db = Database(self.install_path)
-        self.spack_installed_db = spack.installed_db
-        spack.installed_db = self.installed_db
-
-        # make a mock database with some packages installed note that
-        # the ref count for dyninst here will be 3, as it's recycled
-        # across each install.
-        #
-        # Here is what the mock DB looks like:
-        #
-        # o  mpileaks     o  mpileaks'    o  mpileaks''
-        # |\              |\              |\
-        # | o  callpath   | o  callpath'  | o  callpath''
-        # |/|             |/|             |/|
-        # o |  mpich      o |  mpich2     o |  zmpi
-        #   |               |             o |  fake
-        #   |               |               |
-        #   |               |______________/
-        #   | .____________/
-        #   |/
-        #   o  dyninst
-        #   |\
-        #   | o  libdwarf
-        #   |/
-        #   o  libelf
-        #
-
-        # Transaction used to avoid repeated writes.
-        with spack.installed_db.write_transaction():
-            self._mock_install('mpileaks ^mpich')
-            self._mock_install('mpileaks ^mpich2')
-            self._mock_install('mpileaks ^zmpi')
-
-
-    def tearDown(self):
-        super(DatabaseTest, self).tearDown()
-        shutil.rmtree(self.install_path)
-        spack.install_path = self.spack_install_path
-        spack.install_layout = self.spack_install_layout
-        spack.installed_db = self.spack_installed_db
-
-
+class DatabaseTest(MockDatabase):
     def test_005_db_exists(self):
         """Make sure db cache file exists after creating."""
         index_file = join_path(self.install_path, '.spack-db', 'index.yaml')
@@ -156,7 +80,6 @@ class DatabaseTest(MockPackagesTest):
         self.assertTrue(os.path.exists(index_file))
         self.assertTrue(os.path.exists(lock_file))
 
-
     def test_010_all_install_sanity(self):
         """Ensure that the install layout reflects what we think it does."""
         all_specs = spack.install_layout.all_specs()
diff --git a/lib/spack/spack/test/directory_layout.py b/lib/spack/spack/test/directory_layout.py
index 8ad8f1a360..74669fe8a2 100644
--- a/lib/spack/spack/test/directory_layout.py
+++ b/lib/spack/spack/test/directory_layout.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """\
 This test verifies that the Spack directory layout works properly.
diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py
new file mode 100644
index 0000000000..ded1539e18
--- /dev/null
+++ b/lib/spack/spack/test/environment.py
@@ -0,0 +1,97 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import unittest
+import os
+from spack.environment import EnvironmentModifications
+
+
+class EnvironmentTest(unittest.TestCase):
+    def setUp(self):
+        os.environ.clear()
+        os.environ['UNSET_ME'] = 'foo'
+        os.environ['EMPTY_PATH_LIST'] = ''
+        os.environ['PATH_LIST'] = '/path/second:/path/third'
+        os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g'
+
+    def test_set(self):
+        env = EnvironmentModifications()
+        env.set('A', 'dummy value')
+        env.set('B', 3)
+        env.apply_modifications()
+        self.assertEqual('dummy value', os.environ['A'])
+        self.assertEqual(str(3), os.environ['B'])
+
+    def test_unset(self):
+        env = EnvironmentModifications()
+        self.assertEqual('foo', os.environ['UNSET_ME'])
+        env.unset('UNSET_ME')
+        env.apply_modifications()
+        self.assertRaises(KeyError, os.environ.__getitem__, 'UNSET_ME')
+
+    def test_set_path(self):
+        env = EnvironmentModifications()
+        env.set_path('A', ['foo', 'bar', 'baz'])
+        env.apply_modifications()
+        self.assertEqual('foo:bar:baz', os.environ['A'])
+
+    def test_path_manipulation(self):
+        env = EnvironmentModifications()
+
+        env.append_path('PATH_LIST', '/path/last')
+        env.prepend_path('PATH_LIST', '/path/first')
+
+        env.append_path('EMPTY_PATH_LIST', '/path/middle')
+        env.append_path('EMPTY_PATH_LIST', '/path/last')
+        env.prepend_path('EMPTY_PATH_LIST', '/path/first')
+
+        env.append_path('NEWLY_CREATED_PATH_LIST', '/path/middle')
+        env.append_path('NEWLY_CREATED_PATH_LIST', '/path/last')
+        env.prepend_path('NEWLY_CREATED_PATH_LIST', '/path/first')
+
+        env.remove_path('REMOVE_PATH_LIST', '/remove/this')
+        env.remove_path('REMOVE_PATH_LIST', '/duplicate/')
+
+        env.apply_modifications()
+        self.assertEqual('/path/first:/path/second:/path/third:/path/last', os.environ['PATH_LIST'])
+        self.assertEqual('/path/first:/path/middle:/path/last', os.environ['EMPTY_PATH_LIST'])
+        self.assertEqual('/path/first:/path/middle:/path/last', os.environ['NEWLY_CREATED_PATH_LIST'])
+        self.assertEqual('/a/b:/a/c:/a/d:/f/g', os.environ['REMOVE_PATH_LIST'])
+
+    def test_extra_arguments(self):
+        env = EnvironmentModifications()
+        env.set('A', 'dummy value', who='Pkg1')
+        for x in env:
+            assert 'who' in x.args
+        env.apply_modifications()
+        self.assertEqual('dummy value', os.environ['A'])
+
+    def test_extend(self):
+        env = EnvironmentModifications()
+        env.set('A', 'dummy value')
+        env.set('B', 3)
+        copy_construct = EnvironmentModifications(env)
+        self.assertEqual(len(copy_construct), 2)
+        for x, y in zip(env, copy_construct):
+            assert x is y
diff --git a/lib/spack/spack/test/git_fetch.py b/lib/spack/spack/test/git_fetch.py
index 3578044116..4de65760d7 100644
--- a/lib/spack/spack/test/git_fetch.py
+++ b/lib/spack/spack/test/git_fetch.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 
diff --git a/lib/spack/spack/test/hg_fetch.py b/lib/spack/spack/test/hg_fetch.py
index b8a0c1ec46..292ffba949 100644
--- a/lib/spack/spack/test/hg_fetch.py
+++ b/lib/spack/spack/test/hg_fetch.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import spack
diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py
index 8297893f01..cfe6ea9b27 100644
--- a/lib/spack/spack/test/install.py
+++ b/lib/spack/spack/test/install.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import shutil
 import tempfile
@@ -64,7 +64,14 @@ class InstallTest(MockPackagesTest):
         shutil.rmtree(self.tmpdir, ignore_errors=True)
 
 
-    def test_install_and_uninstall(self):
+    def fake_fetchify(self, pkg):
+        """Fake the URL for a package so it downloads from a file."""
+        fetcher = FetchStrategyComposite()
+        fetcher.append(URLFetchStrategy(self.repo.url))
+        pkg.fetcher = fetcher
+
+
+    def ztest_install_and_uninstall(self):
         # Get a basic concrete spec for the trivial install package.
         spec = Spec('trivial_install_test_package')
         spec.concretize()
@@ -73,11 +80,7 @@ class InstallTest(MockPackagesTest):
         # Get the package
         pkg = spack.repo.get(spec)
 
-        # Fake the URL for the package so it downloads from a file.
-
-        fetcher = FetchStrategyComposite()
-        fetcher.append(URLFetchStrategy(self.repo.url))
-        pkg.fetcher = fetcher
+        self.fake_fetchify(pkg)
 
         try:
             pkg.do_install()
@@ -85,3 +88,17 @@ class InstallTest(MockPackagesTest):
         except Exception, e:
             pkg.remove_prefix()
             raise
+
+
+    def test_install_environment(self):
+        spec = Spec('cmake-client').concretized()
+
+        for s in spec.traverse():
+            self.fake_fetchify(s.package)
+
+        pkg = spec.package
+        try:
+            pkg.do_install()
+        except Exception, e:
+            pkg.remove_prefix()
+            raise
diff --git a/lib/spack/spack/test/link_tree.py b/lib/spack/spack/test/link_tree.py
index ee37e765c7..de40991b57 100644
--- a/lib/spack/spack/test/link_tree.py
+++ b/lib/spack/spack/test/link_tree.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import unittest
diff --git a/lib/spack/spack/test/lock.py b/lib/spack/spack/test/lock.py
index 3b11d18da4..0e9f6daf4d 100644
--- a/lib/spack/spack/test/lock.py
+++ b/lib/spack/spack/test/lock.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 These tests ensure that our lock works correctly.
diff --git a/lib/spack/spack/test/make_executable.py b/lib/spack/spack/test/make_executable.py
index a2606acf19..b7a45a3f72 100644
--- a/lib/spack/spack/test/make_executable.py
+++ b/lib/spack/spack/test/make_executable.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 Tests for Spack's built-in parallel make support.
diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py
index e707adfe9d..b682d4e097 100644
--- a/lib/spack/spack/test/mirror.py
+++ b/lib/spack/spack/test/mirror.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import spack
diff --git a/lib/spack/spack/test/mock_database.py b/lib/spack/spack/test/mock_database.py
new file mode 100644
index 0000000000..b1194f2451
--- /dev/null
+++ b/lib/spack/spack/test/mock_database.py
@@ -0,0 +1,104 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import shutil
+import tempfile
+
+import spack
+from spack.spec import Spec
+from spack.database import Database
+from spack.directory_layout import YamlDirectoryLayout
+from spack.test.mock_packages_test import MockPackagesTest
+
+
+class MockDatabase(MockPackagesTest):
+    def _mock_install(self, spec):
+        s = Spec(spec)
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.do_install(fake=True)
+
+    def _mock_remove(self, spec):
+        specs = spack.installed_db.query(spec)
+        assert len(specs) == 1
+        spec = specs[0]
+        spec.package.do_uninstall(spec)
+
+    def setUp(self):
+        super(MockDatabase, self).setUp()
+        #
+        # TODO: make the mockup below easier.
+        #
+
+        # Make a fake install directory
+        self.install_path = tempfile.mkdtemp()
+        self.spack_install_path = spack.install_path
+        spack.install_path = self.install_path
+
+        self.install_layout = YamlDirectoryLayout(self.install_path)
+        self.spack_install_layout = spack.install_layout
+        spack.install_layout = self.install_layout
+
+        # Make fake database and fake install directory.
+        self.installed_db = Database(self.install_path)
+        self.spack_installed_db = spack.installed_db
+        spack.installed_db = self.installed_db
+
+        # make a mock database with some packages installed note that
+        # the ref count for dyninst here will be 3, as it's recycled
+        # across each install.
+        #
+        # Here is what the mock DB looks like:
+        #
+        # o  mpileaks     o  mpileaks'    o  mpileaks''
+        # |\              |\              |\
+        # | o  callpath   | o  callpath'  | o  callpath''
+        # |/|             |/|             |/|
+        # o |  mpich      o |  mpich2     o |  zmpi
+        #   |               |             o |  fake
+        #   |               |               |
+        #   |               |______________/
+        #   | .____________/
+        #   |/
+        #   o  dyninst
+        #   |\
+        #   | o  libdwarf
+        #   |/
+        #   o  libelf
+        #
+
+        # Transaction used to avoid repeated writes.
+        with spack.installed_db.write_transaction():
+            self._mock_install('mpileaks ^mpich')
+            self._mock_install('mpileaks ^mpich2')
+            self._mock_install('mpileaks ^zmpi')
+
+    def tearDown(self):
+        for spec in spack.installed_db.query():
+            spec.package.do_uninstall(spec)
+        super(MockDatabase, self).tearDown()
+        shutil.rmtree(self.install_path)
+        spack.install_path = self.spack_install_path
+        spack.install_layout = self.spack_install_layout
+        spack.installed_db = self.spack_installed_db
diff --git a/lib/spack/spack/test/mock_packages_test.py b/lib/spack/spack/test/mock_packages_test.py
index 81b56daacd..79dbdb89a6 100644
--- a/lib/spack/spack/test/mock_packages_test.py
+++ b/lib/spack/spack/test/mock_packages_test.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import shutil
@@ -107,11 +107,11 @@ compilers:
 mock_packages_config = """\
 packages:
   externaltool:
-    nobuild: True
+    buildable: False
     paths:
       externaltool@1.0%gcc@4.5.0: /path/to/external_tool
   externalvirtual:
-    nobuild: True
+    buildable: False
     paths:
       externalvirtual@2.0%clang@3.3: /path/to/external_virtual_clang
       externalvirtual@1.0%gcc@4.5.0: /path/to/external_virtual_gcc
diff --git a/lib/spack/spack/test/mock_repo.py b/lib/spack/spack/test/mock_repo.py
index a8bdfb5571..a8098b8eec 100644
--- a/lib/spack/spack/test/mock_repo.py
+++ b/lib/spack/spack/test/mock_repo.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import shutil
diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py
new file mode 100644
index 0000000000..c73badf8f2
--- /dev/null
+++ b/lib/spack/spack/test/modules.py
@@ -0,0 +1,181 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import collections
+from contextlib import contextmanager
+
+import StringIO
+import spack.modules
+from spack.test.mock_packages_test import MockPackagesTest
+
+FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
+
+
+# Monkey-patch open to write module files to a StringIO instance
+@contextmanager
+def mock_open(filename, mode):
+    if not mode == 'w':
+        raise RuntimeError(
+            'test.modules : unexpected opening mode for monkey-patched open')
+
+    FILE_REGISTRY[filename] = StringIO.StringIO()
+
+    try:
+        yield FILE_REGISTRY[filename]
+    finally:
+        handle = FILE_REGISTRY[filename]
+        FILE_REGISTRY[filename] = handle.getvalue()
+        handle.close()
+
+
+configuration_autoload_direct = {
+    'enable': ['tcl'],
+    'tcl': {
+        'all': {
+            'autoload': 'direct'
+        }
+    }
+}
+
+configuration_autoload_all = {
+    'enable': ['tcl'],
+    'tcl': {
+        'all': {
+            'autoload': 'all'
+        }
+    }
+}
+
+configuration_alter_environment = {
+    'enable': ['tcl'],
+    'tcl': {
+        'all': {
+            'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']}
+        },
+        'arch=x86-linux': {
+            'environment': {'set': {'FOO': 'foo'},
+                            'unset': ['BAR']}
+        }
+    }
+}
+
+configuration_blacklist = {
+    'enable': ['tcl'],
+    'tcl': {
+        'blacklist': ['callpath'],
+        'all': {
+            'autoload': 'direct'
+        }
+    }
+}
+
+configuration_conflicts = {
+    'enable': ['tcl'],
+    'tcl': {
+        'naming_scheme': '{name}/{version}-{compiler.name}',
+        'all': {
+            'conflict': ['{name}', 'intel/14.0.1']
+        }
+    }
+}
+
+
+class TclTests(MockPackagesTest):
+    def setUp(self):
+        super(TclTests, self).setUp()
+        self.configuration_obj = spack.modules.CONFIGURATION
+        spack.modules.open = mock_open
+        # Make sure that a non-mocked configuration will trigger an error
+        spack.modules.CONFIGURATION = None
+
+    def tearDown(self):
+        del spack.modules.open
+        spack.modules.CONFIGURATION = self.configuration_obj
+        super(TclTests, self).tearDown()
+
+    def get_modulefile_content(self, spec):
+        spec.concretize()
+        generator = spack.modules.TclModule(spec)
+        generator.write()
+        content = FILE_REGISTRY[generator.file_name].split('\n')
+        return content
+
+    def test_simple_case(self):
+        spack.modules.CONFIGURATION = configuration_autoload_direct
+        spec = spack.spec.Spec('mpich@3.0.4 arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertTrue('module-whatis "mpich @3.0.4"' in content)
+
+    def test_autoload(self):
+        spack.modules.CONFIGURATION = configuration_autoload_direct
+        spec = spack.spec.Spec('mpileaks arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 2)
+
+        spack.modules.CONFIGURATION = configuration_autoload_all
+        spec = spack.spec.Spec('mpileaks arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 5)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 5)
+
+    def test_alter_environment(self):
+        spack.modules.CONFIGURATION = configuration_alter_environment
+        spec = spack.spec.Spec('mpileaks arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x
+                 for x in content
+                 if x.startswith('prepend-path CMAKE_PREFIX_PATH')]), 0)
+        self.assertEqual(
+            len([x for x in content if 'setenv FOO "foo"' in x]), 1)
+        self.assertEqual(len([x for x in content if 'unsetenv BAR' in x]), 1)
+
+        spec = spack.spec.Spec('libdwarf arch=x64-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x
+                 for x in content
+                 if x.startswith('prepend-path CMAKE_PREFIX_PATH')]), 0)
+        self.assertEqual(
+            len([x for x in content if 'setenv FOO "foo"' in x]), 0)
+        self.assertEqual(len([x for x in content if 'unsetenv BAR' in x]), 0)
+
+    def test_blacklist(self):
+        spack.modules.CONFIGURATION = configuration_blacklist
+        spec = spack.spec.Spec('mpileaks arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 1)
+
+    def test_conflicts(self):
+        spack.modules.CONFIGURATION = configuration_conflicts
+        spec = spack.spec.Spec('mpileaks arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x for x in content if x.startswith('conflict')]), 2)
+        self.assertEqual(
+            len([x for x in content if x == 'conflict mpileaks']), 1)
+        self.assertEqual(
+            len([x for x in content if x == 'conflict intel/14.0.1']), 1)
diff --git a/lib/spack/spack/test/multimethod.py b/lib/spack/spack/test/multimethod.py
index 6a723d123e..7636bd6c38 100644
--- a/lib/spack/spack/test/multimethod.py
+++ b/lib/spack/spack/test/multimethod.py
@@ -1,33 +1,37 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 Test for multi_method dispatch.
 """
+import unittest
 
 import spack
 from spack.multimethod import *
+from spack.version import *
+from spack.spec import Spec
+from spack.multimethod import when
 from spack.test.mock_packages_test import *
 from spack.version import *
 
@@ -88,6 +92,23 @@ class MultiMethodTest(MockPackagesTest):
         self.assertEqual(pkg.has_a_default(), 'default')
 
 
+#ifdef NEW
+    def test_architecture_match(self):
+        pkg = spack.repo.get('multimethod arch=x86_64')
+        self.assertEqual(pkg.different_by_architecture(), 'x86_64')
+
+        pkg = spack.repo.get('multimethod arch=ppc64')
+        self.assertEqual(pkg.different_by_architecture(), 'ppc64')
+
+        pkg = spack.repo.get('multimethod arch=ppc32')
+        self.assertEqual(pkg.different_by_architecture(), 'ppc32')
+
+        pkg = spack.repo.get('multimethod arch=arm64')
+        self.assertEqual(pkg.different_by_architecture(), 'arm64')
+
+        pkg = spack.repo.get('multimethod arch=macos')
+        self.assertRaises(NoSuchMethodError, pkg.different_by_architecture)
+#else /* not NEW */
     def test_target_match(self):
         platform = spack.architecture.sys_type()
         targets = platform.targets.values()
@@ -100,6 +121,7 @@ class MultiMethodTest(MockPackagesTest):
             self.assertEqual(pkg.different_by_target(), targets[-1].name)
         else:
             self.assertRaises(NoSuchMethodError, pkg.different_by_target)
+#endif /* not NEW */
 
 
     def test_dependency_match(self):
diff --git a/lib/spack/spack/test/namespace_trie.py b/lib/spack/spack/test/namespace_trie.py
index 2023ba6d96..b38ecd6179 100644
--- a/lib/spack/spack/test/namespace_trie.py
+++ b/lib/spack/spack/test/namespace_trie.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://software.llnl.gov/spack
+# For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import unittest
 
diff --git a/lib/spack/spack/test/optional_deps.py b/lib/spack/spack/test/optional_deps.py
index 55f35ea4c9..b5ba0ecf35 100644
--- a/lib/spack/spack/test/optional_deps.py
+++ b/lib/spack/spack/test/optional_deps.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 from spack.spec import Spec
@@ -42,6 +42,13 @@ class ConcretizeTest(MockPackagesTest):
         self.check_normalize('optional-dep-test+a',
                              Spec('optional-dep-test+a', Spec('a')))
 
+        self.check_normalize('optional-dep-test a=true',
+                             Spec('optional-dep-test a=true', Spec('a')))
+
+
+        self.check_normalize('optional-dep-test a=true',
+                             Spec('optional-dep-test+a', Spec('a')))
+
         self.check_normalize('optional-dep-test@1.1',
                              Spec('optional-dep-test@1.1', Spec('b')))
 
diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py
index ee09040d0d..9198986f5d 100644
--- a/lib/spack/spack/test/package_sanity.py
+++ b/lib/spack/spack/test/package_sanity.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """\
 This test does sanity checks on Spack's builtin package database.
diff --git a/lib/spack/spack/test/packages.py b/lib/spack/spack/test/packages.py
index f0b5e05f3b..bea42bb33a 100644
--- a/lib/spack/spack/test/packages.py
+++ b/lib/spack/spack/test/packages.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 import spack
diff --git a/lib/spack/spack/test/pattern.py b/lib/spack/spack/test/pattern.py
index 6c783c6a5f..3419d600b8 100644
--- a/lib/spack/spack/test/pattern.py
+++ b/lib/spack/spack/test/pattern.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 import unittest
diff --git a/lib/spack/spack/test/python_version.py b/lib/spack/spack/test/python_version.py
index 4294975304..6c09effc56 100644
--- a/lib/spack/spack/test/python_version.py
+++ b/lib/spack/spack/test/python_version.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This test ensures that all Spack files are Python version 2.6 or less.
diff --git a/lib/spack/spack/test/sbang.py b/lib/spack/spack/test/sbang.py
index 825bc4be98..6aea1a68c7 100644
--- a/lib/spack/spack/test/sbang.py
+++ b/lib/spack/spack/test/sbang.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """\
 Test that Spack's shebang filtering works correctly.
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index 4ed7de9c7d..3c005c4ead 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 These tests check Spec DAG operations using dummy packages.
@@ -31,6 +31,8 @@ You can find the dummy packages here::
 import spack
 import spack.package
 
+from llnl.util.lang import list_modules
+
 from spack.spec import Spec
 from spack.test.mock_packages_test import *
 
@@ -238,6 +240,12 @@ class SpecDagTest(MockPackagesTest):
         self.assertRaises(spack.spec.UnsatisfiableCompilerSpecError, spec.normalize)
 
 
+#ifdef NEW
+    def test_unsatisfiable_architecture(self):
+        self.set_pkg_dep('mpileaks', 'mpich arch=bgqos_0')
+        spec = Spec('mpileaks ^mpich arch=sles_10_ppc64 ^callpath ^dyninst ^libelf ^libdwarf')
+        self.assertRaises(spack.spec.UnsatisfiableArchitectureSpecError, spec.normalize)
+#else /* not NEW */
     def test_unsatisfiable_target(self):
         platform = spack.architecture.sys_type()
         if len(platform.targets) > 1:
@@ -246,6 +254,7 @@ class SpecDagTest(MockPackagesTest):
             self.set_pkg_dep('mpileaks', 'mpich='+first)
             spec = Spec('mpileaks ^mpich='+ second +' ^callpath ^dyninst ^libelf ^libdwarf')
             self.assertRaises(spack.spec.UnsatisfiableTargetSpecError, spec.normalize)
+#endif /* not NEW */
 
 
     def test_invalid_dep(self):
diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py
index 84d8c0edd8..b6c9d61293 100644
--- a/lib/spack/spack/test/spec_semantics.py
+++ b/lib/spack/spack/test/spec_semantics.py
@@ -1,27 +1,28 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+import unittest
 from spack.spec import *
 from spack.test.mock_packages_test import *
 
@@ -137,11 +138,20 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_unsatisfiable('foo %gcc@4.7', '%gcc@4.7.3')
 
 
+#ifdef NEW
+    def test_satisfies_architecture(self):
+        self.check_satisfies('foo arch=chaos_5_x86_64_ib', ' arch=chaos_5_x86_64_ib')
+        self.check_satisfies('foo arch=bgqos_0', ' arch=bgqos_0')
+
+        self.check_unsatisfiable('foo arch=bgqos_0', ' arch=chaos_5_x86_64_ib')
+        self.check_unsatisfiable('foo arch=chaos_5_x86_64_ib', ' arch=bgqos_0')
+#else /* not NEW */
     def test_satisfies_target(self):
         platform = spack.architecture.sys_type()
         targets = platform.targets.values()
         for target in targets:
             self.check_satisfies('foo='+target.name, '='+target.name)
+#endif /* not NEW */
 
         for i in range(1,len(targets)):
             self.check_unsatisfiable('foo='+targets[i-1].name, '='+targets[i].name)
@@ -191,12 +201,20 @@ class SpecSematicsTest(MockPackagesTest):
     def test_satisfies_matching_variant(self):
         self.check_satisfies('mpich+foo', 'mpich+foo')
         self.check_satisfies('mpich~foo', 'mpich~foo')
+        self.check_satisfies('mpich foo=1', 'mpich foo=1')
+
+        #confirm that synonymous syntax works correctly
+        self.check_satisfies('mpich+foo', 'mpich foo=True')
+        self.check_satisfies('mpich foo=true', 'mpich+foo')
+        self.check_satisfies('mpich~foo', 'mpich foo=FALSE')
+        self.check_satisfies('mpich foo=False', 'mpich~foo')
 
 
     def test_satisfies_unconstrained_variant(self):
         # only asked for mpich, no constraints.  Either will do.
         self.check_satisfies('mpich+foo', 'mpich')
         self.check_satisfies('mpich~foo', 'mpich')
+        self.check_satisfies('mpich foo=1', 'mpich')
 
 
     def test_unsatisfiable_variants(self):
@@ -205,16 +223,44 @@ class SpecSematicsTest(MockPackagesTest):
         # 'mpich' is not concrete:
         self.check_satisfies('mpich', 'mpich+foo', False)
         self.check_satisfies('mpich', 'mpich~foo', False)
+        self.check_satisfies('mpich', 'mpich foo=1', False)
 
         # 'mpich' is concrete:
         self.check_unsatisfiable('mpich', 'mpich+foo', True)
         self.check_unsatisfiable('mpich', 'mpich~foo', True)
+        self.check_unsatisfiable('mpich', 'mpich foo=1', True)
 
 
     def test_unsatisfiable_variant_mismatch(self):
         # No matchi in specs
         self.check_unsatisfiable('mpich~foo', 'mpich+foo')
         self.check_unsatisfiable('mpich+foo', 'mpich~foo')
+        self.check_unsatisfiable('mpich foo=1', 'mpich foo=2')
+
+
+    def test_satisfies_matching_compiler_flag(self):
+        self.check_satisfies('mpich cppflags="-O3"', 'mpich cppflags="-O3"')
+        self.check_satisfies('mpich cppflags="-O3 -Wall"', 'mpich cppflags="-O3 -Wall"')
+
+
+    def test_satisfies_unconstrained_compiler_flag(self):
+        # only asked for mpich, no constraints.  Any will do.
+        self.check_satisfies('mpich cppflags="-O3"', 'mpich')
+
+
+    def test_unsatisfiable_compiler_flag(self):
+        # This case is different depending on whether the specs are concrete.
+
+        # 'mpich' is not concrete:
+        self.check_satisfies('mpich', 'mpich cppflags="-O3"', False)
+
+        # 'mpich' is concrete:
+        self.check_unsatisfiable('mpich', 'mpich cppflags="-O3"', True)
+
+
+    def test_unsatisfiable_compiler_flag_mismatch(self):
+        # No matchi in specs
+        self.check_unsatisfiable('mpich cppflags="-O3"', 'mpich cppflags="-O2"')
 
 
     def test_satisfies_virtual(self):
@@ -302,20 +348,34 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_constrain('libelf+debug+foo', 'libelf+debug', 'libelf+foo')
         self.check_constrain('libelf+debug+foo', 'libelf+debug', 'libelf+debug+foo')
 
+        self.check_constrain('libelf debug=2 foo=1', 'libelf debug=2', 'libelf foo=1')
+        self.check_constrain('libelf debug=2 foo=1', 'libelf debug=2', 'libelf debug=2 foo=1')
+
         self.check_constrain('libelf+debug~foo', 'libelf+debug', 'libelf~foo')
         self.check_constrain('libelf+debug~foo', 'libelf+debug', 'libelf+debug~foo')
 
 
+#ifdef NEW
+    def test_constrain_compiler_flags(self):
+        self.check_constrain('libelf cflags="-O3" cppflags="-Wall"', 'libelf cflags="-O3"', 'libelf cppflags="-Wall"')
+        self.check_constrain('libelf cflags="-O3" cppflags="-Wall"', 'libelf cflags="-O3"', 'libelf cflags="-O3" cppflags="-Wall"')
+
+
+    def test_constrain_arch(self):
+        self.check_constrain('libelf arch=bgqos_0', 'libelf arch=bgqos_0', 'libelf arch=bgqos_0')
+        self.check_constrain('libelf arch=bgqos_0', 'libelf', 'libelf arch=bgqos_0')
+#else /* not NEW */
     def test_constrain_target(self):
         platform = spack.architecture.sys_type()
         target = platform.target('default_target').name
         self.check_constrain('libelf='+target, 'libelf='+target, 'libelf='+target)
         self.check_constrain('libelf='+target, 'libelf', 'libelf='+target)
+#endif /* not NEW */
 
 
     def test_constrain_compiler(self):
-        self.check_constrain('libelf%intel', 'libelf%intel', 'libelf%intel')
-        self.check_constrain('libelf%intel', 'libelf', 'libelf%intel')
+        self.check_constrain('libelf %gcc@4.4.7', 'libelf %gcc@4.4.7', 'libelf %gcc@4.4.7')
+        self.check_constrain('libelf %gcc@4.4.7', 'libelf', 'libelf %gcc@4.4.7')
 
 
     def test_invalid_constraint(self):
@@ -324,11 +384,19 @@ class SpecSematicsTest(MockPackagesTest):
 
         self.check_invalid_constraint('libelf+debug', 'libelf~debug')
         self.check_invalid_constraint('libelf+debug~foo', 'libelf+debug+foo')
+#ifdef NEW
+        self.check_invalid_constraint('libelf debug=2', 'libelf debug=1')
+
+        self.check_invalid_constraint('libelf cppflags="-O3"', 'libelf cppflags="-O2"')
+
+        self.check_invalid_constraint('libelf arch=bgqos_0', 'libelf arch=x86_54')
+#else /* not NEW */
 
         platform = spack.architecture.sys_type()
         targets = platform.targets.values()
         if len(targets) > 1:
             self.check_invalid_constraint('libelf='+targets[0].name, 'libelf='+targets[1].name)
+#endif /* not NEW */
 
 
     def test_constrain_changed(self):
@@ -338,8 +406,14 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_constrain_changed('libelf%gcc', '%gcc@4.5')
         self.check_constrain_changed('libelf', '+debug')
         self.check_constrain_changed('libelf', '~debug')
+#ifdef NEW
+        self.check_constrain_changed('libelf', 'debug=2')
+        self.check_constrain_changed('libelf', 'cppflags="-O3"')
+        self.check_constrain_changed('libelf', ' arch=bgqos_0')
+#else /* not NEW */
         platform = spack.architecture.sys_type()
         self.check_constrain_changed('libelf', '='+platform.target('default_target').name)
+#endif /* not NEW */
 
 
     def test_constrain_not_changed(self):
@@ -350,9 +424,15 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_constrain_not_changed('libelf%gcc@4.5', '%gcc@4.5')
         self.check_constrain_not_changed('libelf+debug', '+debug')
         self.check_constrain_not_changed('libelf~debug', '~debug')
+#ifdef NEW
+        self.check_constrain_not_changed('libelf debug=2', 'debug=2')
+        self.check_constrain_not_changed('libelf cppflags="-O3"', 'cppflags="-O3"')
+        self.check_constrain_not_changed('libelf arch=bgqos_0', ' arch=bgqos_0')
+#else /* not NEW */
         platform = spack.architecture.sys_type()
         default_target = platform.target('default_target').name
         self.check_constrain_not_changed('libelf='+default_target, '='+default_target)
+#endif /* not NEW */
         self.check_constrain_not_changed('libelf^foo', 'libelf^foo')
         self.check_constrain_not_changed('libelf^foo^bar', 'libelf^foo^bar')
 
@@ -364,9 +444,14 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_constrain_changed('libelf^foo%gcc', 'libelf^foo%gcc@4.5')
         self.check_constrain_changed('libelf^foo', 'libelf^foo+debug')
         self.check_constrain_changed('libelf^foo', 'libelf^foo~debug')
+#ifdef NEW
+        self.check_constrain_changed('libelf^foo', 'libelf^foo cppflags="-O3"')
+        self.check_constrain_changed('libelf^foo', 'libelf^foo arch=bgqos_0')
+#else /* not NEW */
         platform = spack.architecture.sys_type()
         default_target = platform.target('default_target').name
         self.check_constrain_changed('libelf^foo', 'libelf^foo='+default_target)
+#endif /* not NEW */
 
 
     def test_constrain_dependency_not_changed(self):
@@ -376,7 +461,13 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_constrain_not_changed('libelf^foo%gcc@4.5', 'libelf^foo%gcc@4.5')
         self.check_constrain_not_changed('libelf^foo+debug', 'libelf^foo+debug')
         self.check_constrain_not_changed('libelf^foo~debug', 'libelf^foo~debug')
+#ifdef NEW
+        self.check_constrain_not_changed('libelf^foo cppflags="-O3"', 'libelf^foo cppflags="-O3"')
+        self.check_constrain_not_changed('libelf^foo arch=bgqos_0', 'libelf^foo arch=bgqos_0')
+
+#else /* not NEW */
         platform = spack.architecture.sys_type()
         default_target = platform.target('default_target').name
         self.check_constrain_not_changed('libelf^foo='+default_target, 'libelf^foo='+default_target)
 
+#endif /* not NEW */
diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py
index 6e08e30e13..c4e4c9cdfe 100644
--- a/lib/spack/spack/test/spec_syntax.py
+++ b/lib/spack/spack/test/spec_syntax.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import unittest
 
@@ -104,6 +104,8 @@ class SpecSyntaxTest(unittest.TestCase):
 
     def test_full_specs(self):
         self.check_parse("mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1+debug~qt_4^stackwalker@8.1_1e")
+        self.check_parse("mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2~qt_4^stackwalker@8.1_1e")
+        self.check_parse('mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1 cppflags="-O3"+debug~qt_4^stackwalker@8.1_1e')
 
     def test_canonicalize(self):
         self.check_parse(
@@ -128,7 +130,10 @@ class SpecSyntaxTest(unittest.TestCase):
 
     def test_duplicate_variant(self):
         self.assertRaises(DuplicateVariantError, self.check_parse, "x@1.2+debug+debug")
-        self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2+debug+debug")
+        self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2+debug debug=true")
+        self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2 debug=false debug=true")
+        self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2 debug=false~debug")
+
 
     def test_duplicate_depdendence(self):
         self.assertRaises(DuplicateDependencyError, self.check_parse, "x ^y ^y")
diff --git a/lib/spack/spack/test/spec_yaml.py b/lib/spack/spack/test/spec_yaml.py
index 11987ea1b3..0230fc203a 100644
--- a/lib/spack/spack/test/spec_yaml.py
+++ b/lib/spack/spack/test/spec_yaml.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Test YAML serialization for specs.
 
diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py
index ea425127c4..6d8c3ac67c 100644
--- a/lib/spack/spack/test/stage.py
+++ b/lib/spack/spack/test/stage.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """\
 Test that the Stage class works correctly.
diff --git a/lib/spack/spack/test/svn_fetch.py b/lib/spack/spack/test/svn_fetch.py
index 1ee4ee700e..0a745a090b 100644
--- a/lib/spack/spack/test/svn_fetch.py
+++ b/lib/spack/spack/test/svn_fetch.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re
diff --git a/lib/spack/spack/test/tally_plugin.py b/lib/spack/spack/test/tally_plugin.py
index 4163ab95dd..96af1c9b21 100644
--- a/lib/spack/spack/test/tally_plugin.py
+++ b/lib/spack/spack/test/tally_plugin.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://scalability-software.llnl.gov/spack
+# For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 
diff --git a/lib/spack/spack/test/unit_install.py b/lib/spack/spack/test/unit_install.py
deleted file mode 100644
index 18615b7efe..0000000000
--- a/lib/spack/spack/test/unit_install.py
+++ /dev/null
@@ -1,126 +0,0 @@
-##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import itertools
-import unittest
-
-import spack
-
-test_install = __import__("spack.cmd.test-install",
-    fromlist=["BuildId", "create_test_output", "TestResult"])
-
-class MockOutput(object):
-    def __init__(self):
-        self.results = {}
-
-    def add_test(self, buildId, passed=True, buildInfo=None):
-        self.results[buildId] = passed
-
-    def write_to(self, stream):
-        pass
-
-class MockSpec(object):
-    def __init__(self, name, version, hashStr=None):
-        self.dependencies = {}
-        self.name = name
-        self.version = version
-        self.hash = hashStr if hashStr else hash((name, version))
-
-    def traverse(self, order=None):
-        allDeps = itertools.chain.from_iterable(i.traverse() for i in
-            self.dependencies.itervalues())
-        return set(itertools.chain([self], allDeps))
-
-    def dag_hash(self):
-        return self.hash
-
-    def to_yaml(self):
-        return "<<<MOCK YAML {0}>>>".format(test_install.BuildId(self).stringId())
-
-class MockPackage(object):
-    def __init__(self, buildLogPath):
-        self.installed = False
-        self.build_log_path = buildLogPath
-
-specX = MockSpec("X", "1.2.0")
-specY = MockSpec("Y", "2.3.8")
-specX.dependencies['Y'] = specY
-pkgX = MockPackage('logX')
-pkgY = MockPackage('logY')
-bIdX = test_install.BuildId(specX)
-bIdY = test_install.BuildId(specY)
-
-class UnitInstallTest(unittest.TestCase):
-    """Tests test-install where X->Y"""
-
-    def setUp(self):
-        super(UnitInstallTest, self).setUp()
-
-        pkgX.installed = False
-        pkgY.installed = False
-
-        self.saved_db = spack.repo
-        pkgDb = MockPackageDb({specX:pkgX, specY:pkgY})
-        spack.repo = pkgDb
-
-
-    def tearDown(self):
-        super(UnitInstallTest, self).tearDown()
-
-        spack.repo = self.saved_db
-
-    def test_installing_both(self):
-        mo = MockOutput()
-
-        pkgX.installed = True
-        pkgY.installed = True
-        test_install.create_test_output(specX, [specX, specY], mo, getLogFunc=mock_fetch_log)
-
-        self.assertEqual(mo.results,
-            {bIdX:test_install.TestResult.PASSED,
-             bIdY:test_install.TestResult.PASSED})
-
-
-    def test_dependency_already_installed(self):
-        mo = MockOutput()
-
-        pkgX.installed = True
-        pkgY.installed = True
-        test_install.create_test_output(specX, [specX], mo, getLogFunc=mock_fetch_log)
-        self.assertEqual(mo.results, {bIdX:test_install.TestResult.PASSED})
-
-    #TODO: add test(s) where Y fails to install
-
-
-class MockPackageDb(object):
-    def __init__(self, init=None):
-        self.specToPkg = {}
-        if init:
-            self.specToPkg.update(init)
-
-    def get(self, spec):
-        return self.specToPkg[spec]
-
-def mock_fetch_log(path):
-    return []
diff --git a/lib/spack/spack/test/url_extrapolate.py b/lib/spack/spack/test/url_extrapolate.py
index 068a335b49..ffd4230f71 100644
--- a/lib/spack/spack/test/url_extrapolate.py
+++ b/lib/spack/spack/test/url_extrapolate.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """\
 Tests ability of spack to extrapolate URL versions from existing versions.
diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py
index 561d4658a1..648996aaaa 100644
--- a/lib/spack/spack/test/url_parse.py
+++ b/lib/spack/spack/test/url_parse.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """\
 This file has a bunch of versions tests taken from the excellent version
diff --git a/lib/spack/spack/test/url_substitution.py b/lib/spack/spack/test/url_substitution.py
index 2be38af0d3..9cc04834b6 100644
--- a/lib/spack/spack/test/url_substitution.py
+++ b/lib/spack/spack/test/url_substitution.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """\
 This test does sanity checks on substituting new versions into URLs
diff --git a/lib/spack/spack/test/versions.py b/lib/spack/spack/test/versions.py
index 2732006eb3..a026403e2e 100644
--- a/lib/spack/spack/test/versions.py
+++ b/lib/spack/spack/test/versions.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 These version tests were taken from the RPM source code.
diff --git a/lib/spack/spack/test/yaml.py b/lib/spack/spack/test/yaml.py
index b930c022f2..f1b83e7b71 100644
--- a/lib/spack/spack/test/yaml.py
+++ b/lib/spack/spack/test/yaml.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 Test Spack's custom YAML format.
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
index ad551a6ded..f678a2dca9 100644
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This module has methods for parsing names and versions of packages from URLs.
@@ -142,7 +142,7 @@ def split_url_extension(path):
 
 def downloaded_file_extension(path):
     """This returns the type of archive a URL refers to.  This is
-       sometimes confusing becasue of URLs like:
+       sometimes confusing because of URLs like:
 
            (1) https://github.com/petdance/ack/tarball/1.93_02
 
@@ -206,6 +206,9 @@ def parse_version_offset(path):
         # e.g. lame-398-1
         (r'-((\d)+-\d)', stem),
 
+        # e.g. foobar_1.2-3
+        (r'_((\d+\.)+\d+(-\d+)?[a-z]?)', stem),
+
         # e.g. foobar-4.5.1
         (r'-((\d+\.)*\d+)$', stem),
 
diff --git a/lib/spack/spack/util/__init__.py b/lib/spack/spack/util/__init__.py
index b54691b67c..ed1ec23bca 100644
--- a/lib/spack/spack/util/__init__.py
+++ b/lib/spack/spack/util/__init__.py
@@ -1,24 +1,24 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py
index ea1f233bce..dc1188eb0f 100644
--- a/lib/spack/spack/util/compression.py
+++ b/lib/spack/spack/util/compression.py
@@ -1,39 +1,38 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
 import os
 from itertools import product
 from spack.util.executable import which
 
-# Supported archvie extensions.
+# Supported archive extensions.
 PRE_EXTS = ["tar"]
 EXTS     = ["gz", "bz2", "xz", "Z", "zip", "tgz"]
 
-# Add EXTS last so that .tar.gz is matched *before* tar.gz
-ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product(PRE_EXTS, EXTS)] + EXTS
-
+# Add PRE_EXTS and EXTS last so that .tar.gz is matched *before* .tar or .gz
+ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product(PRE_EXTS, EXTS)] + PRE_EXTS + EXTS
 
 def allowed_archive(path):
     return any(path.endswith(t) for t in ALLOWED_ARCHIVE_TYPES)
diff --git a/lib/spack/spack/util/crypto.py b/lib/spack/spack/util/crypto.py
index 5269260284..1ae9793518 100644
--- a/lib/spack/spack/util/crypto.py
+++ b/lib/spack/spack/util/crypto.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import hashlib
 
diff --git a/lib/spack/spack/util/debug.py b/lib/spack/spack/util/debug.py
index 7930753f6f..e8a0595416 100644
--- a/lib/spack/spack/util/debug.py
+++ b/lib/spack/spack/util/debug.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Debug signal handler: prints a stack trace and enters interpreter.
 
diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py
index ae8e5708be..f23110d2d9 100644
--- a/lib/spack/spack/util/environment.py
+++ b/lib/spack/spack/util/environment.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 
@@ -59,14 +59,8 @@ def path_put_first(var_name, directories):
     path_set(var_name, new_path)
 
 
-def pop_keys(dictionary, *keys):
-    for key in keys:
-        if key in dictionary:
-            dictionary.pop(key)
-
-
 def dump_environment(path):
     """Dump the current environment out to a file."""
     with open(path, 'w') as env_file:
-        for key,val in sorted(os.environ.items()):
+        for key, val in sorted(os.environ.items()):
             env_file.write("%s=%s\n" % (key, val))
diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py
index c349d071d2..14b56e8d6c 100644
--- a/lib/spack/spack/util/executable.py
+++ b/lib/spack/spack/util/executable.py
@@ -1,31 +1,29 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-__all__ = ['Executable', 'which', 'ProcessError']
 
 import os
-import sys
 import re
 import subprocess
 import inspect
@@ -34,9 +32,12 @@ import llnl.util.tty as tty
 import spack
 import spack.error
 
+__all__ = ['Executable', 'which', 'ProcessError']
+
 
 class Executable(object):
     """Class representing a program that can be run on the command line."""
+
     def __init__(self, name):
         self.exe = name.split(' ')
         self.returncode = None
@@ -44,16 +45,13 @@ class Executable(object):
         if not self.exe:
             raise ProcessError("Cannot construct executable for '%s'" % name)
 
-
     def add_default_arg(self, arg):
         self.exe.append(arg)
 
-
     @property
     def command(self):
         return ' '.join(self.exe)
 
-
     def __call__(self, *args, **kwargs):
         """Run this executable in a subprocess.
 
@@ -105,6 +103,8 @@ class Executable(object):
         fail_on_error = kwargs.pop("fail_on_error", True)
         ignore_errors = kwargs.pop("ignore_errors", ())
 
+        env = kwargs.get('env', None)
+
         # TODO: This is deprecated.  Remove in a future version.
         return_output = kwargs.pop("return_output", False)
 
@@ -114,8 +114,8 @@ class Executable(object):
         else:
             output = kwargs.pop("output", None)
 
-        error         = kwargs.pop("error", None)
-        input         = kwargs.pop("input", None)
+        error = kwargs.pop("error", None)
+        input = kwargs.pop("input", None)
         if input is str:
             raise ValueError("Cannot use `str` as input stream.")
 
@@ -126,86 +126,91 @@ class Executable(object):
                 return subprocess.PIPE, False
             else:
                 return arg, False
+
         ostream, close_ostream = streamify(output, 'w')
-        estream, close_estream = streamify(error,  'w')
-        istream, close_istream = streamify(input,  'r')
+        estream, close_estream = streamify(error, 'w')
+        istream, close_istream = streamify(input, 'r')
 
         # if they just want to ignore one error code, make it a tuple.
         if isinstance(ignore_errors, int):
-            ignore_errors = (ignore_errors,)
+            ignore_errors = (ignore_errors, )
 
         quoted_args = [arg for arg in args if re.search(r'^"|^\'|"$|\'$', arg)]
         if quoted_args:
-            tty.warn("Quotes in command arguments can confuse scripts like configure.",
-                     "The following arguments may cause problems when executed:",
-                     str("\n".join(["    "+arg for arg in quoted_args])),
-                     "Quotes aren't needed because spack doesn't use a shell.",
-                     "Consider removing them")
+            tty.warn(
+                "Quotes in command arguments can confuse scripts like"
+                " configure.",
+                "The following arguments may cause problems when executed:",
+                str("\n".join(["    " + arg for arg in quoted_args])),
+                "Quotes aren't needed because spack doesn't use a shell.",
+                "Consider removing them")
 
         cmd = self.exe + list(args)
 
-        cmd_line = ' '.join(cmd)
+        cmd_line = "'%s'" % "' '".join(
+            map(lambda arg: arg.replace("'", "'\"'\"'"), cmd))
         tty.debug(cmd_line)
 
         try:
             proc = subprocess.Popen(
-                cmd, stdin=istream, stderr=estream, stdout=ostream)
+                cmd,
+                stdin=istream,
+                stderr=estream,
+                stdout=ostream,
+                env=env)
             out, err = proc.communicate()
 
             rc = self.returncode = proc.returncode
             if fail_on_error and rc != 0 and (rc not in ignore_errors):
-                raise ProcessError("Command exited with status %d:"
-                                   % proc.returncode, cmd_line)
+                raise ProcessError("Command exited with status %d:" %
+                                   proc.returncode, cmd_line)
 
 
             if output is str or error is str:
                 result = ''
-                if output is str: result += out
-                if error is str:  result += err
+                if output is str:
+                    result += out
+                if error is str:
+                    result += err
                 return result
 
         except OSError, e:
             raise ProcessError(
-                "%s: %s" % (self.exe[0], e.strerror),
-                "Command: " + cmd_line)
+                "%s: %s" % (self.exe[0], e.strerror), "Command: " + cmd_line)
 
         except subprocess.CalledProcessError, e:
             if fail_on_error:
                 raise ProcessError(
-                    str(e),
-                    "\nExit status %d when invoking command: %s"
-                    % (proc.returncode, cmd_line))
+                    str(e), "\nExit status %d when invoking command: %s" %
+                    (proc.returncode, cmd_line))
 
         finally:
-            if close_ostream: output.close()
-            if close_estream: error.close()
-            if close_istream: input.close()
-
+            if close_ostream:
+                output.close()
+            if close_estream:
+                error.close()
+            if close_istream:
+                input.close()
 
     def __eq__(self, other):
         return self.exe == other.exe
 
-
     def __neq__(self, other):
         return not (self == other)
 
-
     def __hash__(self):
-        return hash((type(self),) + tuple(self.exe))
-
+        return hash((type(self), ) + tuple(self.exe))
 
     def __repr__(self):
         return "<exe: %s>" % self.exe
 
-
     def __str__(self):
         return ' '.join(self.exe)
 
 
-
 def which(name, **kwargs):
     """Finds an executable in the path like command-line which."""
-    path     = kwargs.get('path', os.environ.get('PATH', '').split(os.pathsep))
+    path = kwargs.get('path', os.environ.get('PATH', '').split(os.pathsep))
     required = kwargs.get('required', False)
 
     if not path:
@@ -234,14 +239,16 @@ class ProcessError(spack.error.SpackError):
     @property
     def long_message(self):
         msg = self._long_message
-        if msg: msg += "\n\n"
+        if msg:
+            msg += "\n\n"
 
         if self.build_log:
             msg += "See build log for details:\n"
             msg += "  %s" % self.build_log
 
         if self.package_context:
-            if msg: msg += "\n\n"
+            if msg:
+                msg += "\n\n"
             msg += '\n'.join(self.package_context)
 
         return msg
@@ -268,7 +275,7 @@ def _get_package_context():
         frame = f[0]
 
         # Find a frame with 'self' in the local variables.
-        if not 'self' in frame.f_locals:
+        if 'self' not in frame.f_locals:
             continue
 
         # Look only at a frame in a subclass of spack.Package
@@ -281,9 +288,8 @@ def _get_package_context():
 
     # Build a message showing where in install we failed.
     lines.append("%s:%d, in %s:" % (
-        inspect.getfile(frame.f_code),
-        frame.f_lineno,
-        frame.f_code.co_name))
+        inspect.getfile(frame.f_code), frame.f_lineno, frame.f_code.co_name
+    ))
 
     sourcelines, start = inspect.getsourcelines(frame)
     for i, line in enumerate(sourcelines):
diff --git a/lib/spack/spack/util/multiproc.py b/lib/spack/spack/util/multiproc.py
index 8ca82df011..038cd90121 100644
--- a/lib/spack/spack/util/multiproc.py
+++ b/lib/spack/spack/util/multiproc.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This implements a parallel map operation but it can accept more values
diff --git a/lib/spack/spack/util/naming.py b/lib/spack/spack/util/naming.py
index 5025f15027..2d9762942d 100644
--- a/lib/spack/spack/util/naming.py
+++ b/lib/spack/spack/util/naming.py
@@ -1,3 +1,27 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 # Need this because of spack.util.string
 from __future__ import absolute_import
 import string
diff --git a/lib/spack/spack/util/pattern.py b/lib/spack/spack/util/pattern.py
index 17a126498b..6d4bcb1039 100644
--- a/lib/spack/spack/util/pattern.py
+++ b/lib/spack/spack/util/pattern.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import inspect
 import collections
diff --git a/lib/spack/spack/util/prefix.py b/lib/spack/spack/util/prefix.py
index c613ca5182..e1a0f2958b 100644
--- a/lib/spack/spack/util/prefix.py
+++ b/lib/spack/spack/util/prefix.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This file contains utilities to help with installing packages.
diff --git a/lib/spack/spack/util/spack_yaml.py b/lib/spack/spack/util/spack_yaml.py
index 728e86b8ee..909f9a57a8 100644
--- a/lib/spack/spack/util/spack_yaml.py
+++ b/lib/spack/spack/util/spack_yaml.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Enhanced YAML parsing for Spack.
 
diff --git a/lib/spack/spack/util/string.py b/lib/spack/spack/util/string.py
index 1556ce6d29..ce017b8126 100644
--- a/lib/spack/spack/util/string.py
+++ b/lib/spack/spack/util/string.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 def comma_list(sequence, article=''):
diff --git a/lib/spack/spack/util/web.py b/lib/spack/spack/util/web.py
index 73f4858b02..47abc507e0 100644
--- a/lib/spack/spack/util/web.py
+++ b/lib/spack/spack/util/web.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
 import os
diff --git a/lib/spack/spack/variant.py b/lib/spack/spack/variant.py
index 8959e76684..ad875f5ef5 100644
--- a/lib/spack/spack/variant.py
+++ b/lib/spack/spack/variant.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Variant is a class describing flags on builds, or "variants".
 
@@ -32,5 +32,5 @@ currently variants are just flags.
 class Variant(object):
     """Represents a variant on a build.  Can be either on or off."""
     def __init__(self, default, description):
-        self.default     = bool(default)
+        self.default     = default
         self.description = str(description)
diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py
index e8a0a261c9..247f6d2362 100644
--- a/lib/spack/spack/version.py
+++ b/lib/spack/spack/version.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This module implements Version and version-ish objects.  These are:
diff --git a/lib/spack/spack/virtual.py b/lib/spack/spack/virtual.py
index d16aea8642..bb8333f023 100644
--- a/lib/spack/spack/virtual.py
+++ b/lib/spack/spack/virtual.py
@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 The ``virtual`` module contains utility classes for virtual dependencies.
@@ -67,10 +67,15 @@ class ProviderIndex(object):
         if type(spec) != spack.spec.Spec:
             spec = spack.spec.Spec(spec)
 
+        if not spec.name:
+            # Empty specs do not have a package
+            return
+
         assert(not spec.virtual)
 
         pkg = spec.package
         for provided_spec, provider_spec in pkg.provided.iteritems():
+            provider_spec.compiler_flags = spec.compiler_flags.copy()#We want satisfaction other than flags
             if provider_spec.satisfies(spec, deps=False):
                 provided_name = provided_spec.name