Merge branch 'develop' into features/external-packages

Conflicts:
	lib/spack/spack/package.py

148 files changed, 3131 insertions, 1236 deletions

diff --git a/.mailmap b/.mailmap
index 1b99da32b5..39ec183241 100644
--- a/.mailmap
+++ b/.mailmap
@@ -1,13 +1,20 @@
 Todd Gamblin       <tgamblin@llnl.gov>          George Todd Gamblin <gamblin2@llnl.gov>
+Todd Gamblin       <tgamblin@llnl.gov>          Todd Gamblin        <gamblin2@llnl.gov>
 Adam Moody         <moody20@llnl.gov>           Adam T. Moody       <moody20@llnl.gov>
 Alfredo Gimenez    <gimenez1@llnl.gov>          Alfredo Gimenez     <alfredo.gimenez@gmail.com>
 David Boehme       <boehme3@llnl.gov>           David Boehme        <boehme3@sierra324.llnl.gov>
 David Boehme       <boehme3@llnl.gov>           David Boehme        <boehme3@sierra648.llnl.gov>
 Kevin Brandstatter <kjbrandstatter@gmail.com>   Kevin Brandstatter  <kbrandst@hawk.iit.edu>
 Luc Jaulmes        <luc.jaulmes@bsc.es>         Luc Jaulmes         <jaulmes1@llnl.gov>
-Saravan Pantham    <saravan.pantham@gmail.com>  Saravan Pantham     <pantham1@surface86.llnl.gov
+Saravan Pantham    <saravan.pantham@gmail.com>  Saravan Pantham     <pantham1@surface86.llnl.gov>
 Tom Scogland       <tscogland@llnl.gov>         Tom Scogland        <scogland1@llnl.gov>
 Tom Scogland       <tscogland@llnl.gov>         Tom Scogland        <tom.scogland@gmail.com>
 Joachim Protze     <protze@rz.rwth-aachen.de>   jprotze             <protze@rz.rwth-aachen.de>
 Gregory L. Lee     <lee218@llnl.gov>            Gregory L. Lee      <lee218@surface86.llnl.gov>
+Gregory L. Lee     <lee218@llnl.gov>            Gregory L. Lee      <lee218@cab687.llnl.gov>
+Gregory L. Lee     <lee218@llnl.gov>            Gregory L. Lee      <lee218@cab690.llnl.gov>
+Gregory L. Lee     <lee218@llnl.gov>            Gregory L. Lee      <lee218@catalyst159.llnl.gov>
 Gregory L. Lee     <lee218@llnl.gov>            Gregory Lee         <lee218@llnl.gov>
+Massimiliano Culpo <massimiliano.culpo@epfl.ch> Massimiliano Culpo  <massimiliano.culpo@googlemail.com>
+Massimiliano Culpo <massimiliano.culpo@epfl.ch> alalazo             <massimiliano.culpo@googlemail.com>
+Mark Miller        <miller86@llnl.gov>          miller86            <miller86@llnl.gov>
diff --git a/README.md b/README.md
index bdce345764..8664953c0c 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@ written in pure Python, and specs allow package authors to write a
 single build script for many different builds of the same package.
 
 See the
-[Feature Overview](http://llnl.github.io/spack/features.html)
+[Feature Overview](http://software.llnl.gov/spack/features.html)
 for examples and highlights.
 
 To install spack and install your first package:
@@ -31,7 +31,7 @@ To install spack and install your first package:
 Documentation
 ----------------
 
-[**Full documentation**](http://llnl.github.io/spack) for Spack is
+[**Full documentation**](http://software.llnl.gov/spack) for Spack is
 the first place to look.
 
 See also:
diff --git a/bin/sbang b/bin/sbang
new file mode 100755
index 0000000000..ebfbe2e7a1
--- /dev/null
+++ b/bin/sbang
@@ -0,0 +1,84 @@
+#!/bin/bash
+#
+# `sbang`: Run scripts with long shebang lines.
+#
+# Many operating systems limit the length of shebang lines, making it
+# hard to use interpreters that are deep in the directory hierarchy.
+# `sbang` can run such scripts, either as a shebang interpreter, or
+# directly on the command line.
+#
+# Usage
+# -----------------------------
+# Suppose you have a script, long-shebang.sh, like this:
+#
+#     1    #!/very/long/path/to/some/interpreter
+#     2
+#     3    echo "success!"
+#
+# Invoking this script will result in an error on some OS's.  On
+# Linux, you get this:
+#
+#     $ ./long-shebang.sh
+#     -bash: ./long: /very/long/path/to/some/interp: bad interpreter:
+#            No such file or directory
+#
+# On Mac OS X, the system simply assumes the interpreter is the shell
+# and tries to run with it, which is likely not what you want.
+#
+#
+# `sbang` on the command line
+# -----------------------------
+# You can use `sbang` in two ways.  The first is to use it directly,
+# from the command line, like this:
+#
+#     $ sbang ./long-shebang.sh
+#     success!
+#
+#
+# `sbang` as the interpreter
+# -----------------------------
+# You can also use `sbang` *as* the interpreter for your script. Put
+# `#!/bin/bash /path/to/sbang` on line 1, and move the original
+# shebang to line 2 of the script:
+#
+#     1    #!/bin/bash /path/to/sbang
+#     2    #!/long/path/to/real/interpreter with arguments
+#     3
+#     4    echo "success!"
+#
+#     $ ./long-shebang.sh
+#     success!
+#
+# On Linux, you could shorten line 1 to `#!/path/to/sbang`, but other
+# operating systems like Mac OS X require the interpreter to be a
+# binary, so it's best to use `sbang` as a `bash` argument.
+# Obviously, for this to work, `sbang` needs to have a short enough
+# path that *it* will run without hitting OS limits.
+#
+#
+# How it works
+# -----------------------------
+# `sbang` is a very simple bash script. It looks at the first two
+# lines of a script argument and runs the last line starting with
+# `#!`, with the script as an argument. It also forwards arguments.
+#
+
+# First argument is the script we want to actually run.
+script="$1"
+
+# Search the first two lines of script for interpreters.
+lines=0
+while read line && ((lines < 2)) ; do
+    if [[ "$line" = '#!'* ]]; then
+        interpreter="${line#\#!}"
+    fi
+    lines=$((lines+1))
+done < "$script"
+
+# Invoke any interpreter found, or raise an error if none was found.
+if [ -n "$interpreter" ]; then
+    exec $interpreter "$@"
+else
+    echo "error: sbang found no interpreter in $script"
+    exit 1
+fi
diff --git a/bin/spack b/bin/spack
index 93263217ac..31165bba9d 100755
--- a/bin/spack
+++ b/bin/spack
@@ -42,9 +42,9 @@ SPACK_EXTERNAL_LIBS = os.path.join(SPACK_LIB_PATH, "external")
 sys.path.insert(0, SPACK_EXTERNAL_LIBS)
 
 import warnings
-# Avoid warnings when nose is installed with the python exe being used to run 
-# spack. Note this must be done after Spack's external libs directory is added 
-# to sys.path. 
+# Avoid warnings when nose is installed with the python exe being used to run
+# spack. Note this must be done after Spack's external libs directory is added
+# to sys.path.
 with warnings.catch_warnings():
     warnings.filterwarnings("ignore", ".*nose was already imported")
     import nose
@@ -62,7 +62,7 @@ for pyc_file in orphaned_pyc_files:
     try:
         os.remove(pyc_file)
     except OSError as e:
-        print "WARNING: Spack may fail mysteriously. Couldn't remove orphaned .pyc file: %s" % pyc
+        print "WARNING: Spack may fail mysteriously. Couldn't remove orphaned .pyc file: %s" % pyc_file
 
 # If there is no working directory, use the spack prefix.
 try:
diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index 5d5438220c..accf09cc2a 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -903,7 +903,7 @@ Or, similarly with modules, you could type:
    $ spack load mpich %gcc@4.4.7
 
 These commands will add appropriate directories to your ``PATH``,
-``MANPATH``, and ``LD_LIBRARY_PATH``.  When you no longer want to use
+``MANPATH``, ``CPATH``, and ``LD_LIBRARY_PATH``.  When you no longer want to use
 a package, you can type unload or unuse similarly:
 
 .. code-block:: sh
diff --git a/lib/spack/docs/developer_guide.rst b/lib/spack/docs/developer_guide.rst
index db47de80f5..0b618aa683 100644
--- a/lib/spack/docs/developer_guide.rst
+++ b/lib/spack/docs/developer_guide.rst
@@ -73,19 +73,32 @@ with a high level view of Spack's directory structure::
   spack/                  <- installation root
      bin/
         spack             <- main spack executable
+
+     etc/
+        spack/            <- Spack config files.
+                             Can be overridden by files in ~/.spack.
+
      var/
         spack/            <- build & stage directories
+        repos/            <- contains package repositories
+           builtin/       <- pkg repository that comes with Spack
+              repo.yaml   <- descriptor for the builtin repository
+              packages/   <- directories under here contain packages
+
      opt/
         spack/            <- packages are installed here
+
      lib/
         spack/
            docs/          <- source for this documentation
            env/           <- compiler wrappers for build environment
 
+           external/      <- external libs included in Spack distro
+           llnl/          <- some general-use libraries
+
            spack/         <- spack module; contains Python code
               cmd/        <- each file in here is a spack subcommand
               compilers/  <- compiler description files
-              packages/   <- each file in here is a spack package
               test/       <- unit test modules
               util/       <- common code
 
diff --git a/lib/spack/docs/features.rst b/lib/spack/docs/features.rst
index fcb810086d..0998ba8da4 100644
--- a/lib/spack/docs/features.rst
+++ b/lib/spack/docs/features.rst
@@ -103,7 +103,7 @@ creates a simple python file:
 It doesn't take much python coding to get from there to a working
 package:
 
-.. literalinclude:: ../../../var/spack/packages/libelf/package.py
+.. literalinclude:: ../../../var/spack/repos/builtin/packages/libelf/package.py
    :lines: 25-
 
 Spack also provides wrapper functions around common commands like
diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst
index 67ca18e71a..2c5b68ea65 100644
--- a/lib/spack/docs/getting_started.rst
+++ b/lib/spack/docs/getting_started.rst
@@ -22,7 +22,7 @@ go:
    $ spack install libelf
 
 For a richer experience, use Spack's `shell support
-<http://llnl.github.io/spack/basic_usage.html#environment-modules>`_:
+<http://software.llnl.gov/spack/basic_usage.html#environment-modules>`_:
 
 .. code-block:: sh
 
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 5094f739c4..f368d0a4fa 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -84,7 +84,7 @@ always choose to download just one tarball initially, and run
 
    If it fails entirely, you can get minimal boilerplate by using
    :ref:`spack-edit-f`, or you can manually create a directory and
-   ``package.py`` file for the package in ``var/spack/packages``.
+   ``package.py`` file for the package in ``var/spack/repos/builtin/packages``.
 
 .. note::
 
@@ -203,7 +203,7 @@ edit`` command:
 So, if you used ``spack create`` to create a package, then saved and
 closed the resulting file, you can get back to it with ``spack edit``.
 The ``cmake`` package actually lives in
-``$SPACK_ROOT/var/spack/packages/cmake/package.py``, but this provides
+``$SPACK_ROOT/var/spack/repos/builtin/packages/cmake/package.py``, but this provides
 a much simpler shortcut and saves you the trouble of typing the full
 path.
 
@@ -269,18 +269,18 @@ live in Spack's directory structure.  In general, `spack-create`_ and
 `spack-edit`_ handle creating package files for you, so you can skip
 most of the details here.
 
-``var/spack/packages``
+``var/spack/repos/builtin/packages``
 ~~~~~~~~~~~~~~~~~~~~~~~
 
 A Spack installation directory is structured like a standard UNIX
 install prefix (``bin``, ``lib``, ``include``, ``var``, ``opt``,
 etc.).  Most of the code for Spack lives in ``$SPACK_ROOT/lib/spack``.
-Packages themselves live in ``$SPACK_ROOT/var/spack/packages``.
+Packages themselves live in ``$SPACK_ROOT/var/spack/repos/builtin/packages``.
 
 If you ``cd`` to that directory, you will see directories for each
 package:
 
-.. command-output::  cd $SPACK_ROOT/var/spack/packages;  ls -CF
+.. command-output::  cd $SPACK_ROOT/var/spack/repos/builtin/packages;  ls -CF
    :shell:
    :ellipsis: 10
 
@@ -288,7 +288,7 @@ Each directory contains a file called ``package.py``, which is where
 all the python code for the package goes.  For example, the ``libelf``
 package lives in::
 
-   $SPACK_ROOT/var/spack/packages/libelf/package.py
+   $SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py
 
 Alongside the ``package.py`` file, a package may contain extra
 directories or files (like patches) that it needs to build.
@@ -301,7 +301,7 @@ Packages are named after the directory containing ``package.py``.  So,
 ``libelf``'s ``package.py`` lives in a directory called ``libelf``.
 The ``package.py`` file defines a class called ``Libelf``, which
 extends Spack's ``Package`` class.  for example, here is
-``$SPACK_ROOT/var/spack/packages/libelf/package.py``:
+``$SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py``:
 
 .. code-block:: python
    :linenos:
@@ -328,7 +328,7 @@ these:
    $ spack install libelf@0.8.13
 
 Spack sees the package name in the spec and looks for
-``libelf/package.py`` in ``var/spack/packages``.  Likewise, if you say
+``libelf/package.py`` in ``var/spack/repos/builtin/packages``.  Likewise, if you say
 ``spack install py-numpy``, then Spack looks for
 ``py-numpy/package.py``.
 
@@ -401,6 +401,35 @@ construct the new one for ``8.2.1``.
 When you supply a custom URL for a version, Spack uses that URL
 *verbatim* and does not perform extrapolation.
 
+Skipping the expand step
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Spack normally expands archives automatically after downloading
+them. If you want to skip this step (e.g., for self-extracting
+executables and other custom archive types), you can add
+``expand=False`` to a ``version`` directive.
+
+.. code-block:: python
+
+   version('8.2.1', '4136d7b4c04df68b686570afa26988ac',
+           url='http://example.com/foo-8.2.1-special-version.tar.gz', 'expand=False')
+
+When ``expand`` is set to ``False``, Spack sets the current working
+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
+archives.  The example sets permissions on the downloaded file to make
+it executable, then runs it with some arguments.
+
+.. code-block:: python
+
+   def install(self, spec, prefix):
+       set_executable(self.stage.archive_file)
+       installer = Executable(self.stage.archive_file)
+       installer('--prefix=%s' % prefix, 'arg1', 'arg2', 'etc.')
+
 Checksums
 ~~~~~~~~~~~~~~~~~
 
@@ -703,7 +732,7 @@ supply is a filename, then the patch needs to live within the spack
 source tree.  For example, the patch above lives in a directory
 structure like this::
 
-   $SPACK_ROOT/var/spack/packages/
+   $SPACK_ROOT/var/spack/repos/builtin/packages/
        mvapich2/
            package.py
            ad_lustre_rwcontig_open_source.patch
@@ -1597,7 +1626,7 @@ The last element of a package is its ``install()`` method.  This is
 where the real work of installation happens, and it's the main part of
 the package you'll need to customize for each piece of software.
 
-.. literalinclude::  ../../../var/spack/packages/libelf/package.py
+.. literalinclude::  ../../../var/spack/repos/builtin/packages/libelf/package.py
    :start-after: 0.8.12
    :linenos:
 
@@ -1775,15 +1804,15 @@ 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``
+  * ``-Wl,-rpath,$dep_prefix/lib``
+  * ``-Wl,-rpath,$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 ``-Wl,-rpath,$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
@@ -2172,6 +2201,15 @@ Filtering functions
 
   Examples:
 
+  #. Filtering a Makefile to force it to use Spack's compiler wrappers:
+
+     .. code-block:: python
+
+        filter_file(r'^CC\s*=.*',  spack_cc,  'Makefile')
+        filter_file(r'^CXX\s*=.*', spack_cxx, 'Makefile')
+        filter_file(r'^F77\s*=.*', spack_f77, 'Makefile')
+        filter_file(r'^FC\s*=.*',  spack_fc,  'Makefile')
+
   #. Replacing ``#!/usr/bin/perl`` with ``#!/usr/bin/env perl`` in ``bib2xhtml``:
 
      .. code-block:: python
diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index aacba996b3..a19346ce97 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -90,15 +90,15 @@ case "$command" in
         command="$SPACK_CC"
         language="C"
         ;;
-    c++|CC|g++|clang++|icpc|pgCC|xlc++)
+    c++|CC|g++|clang++|icpc|pgc++|xlc++)
         command="$SPACK_CXX"
         language="C++"
         ;;
-    f90|fc|f95|gfortran|ifort|pgf90|xlf90|nagfor)
+    f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor)
         command="$SPACK_FC"
         language="Fortran 90"
         ;;
-    f77|gfortran|ifort|pgf77|xlf|nagfor)
+    f77|gfortran|ifort|pgfortran|xlf|nagfor)
         command="$SPACK_F77"
         language="Fortran 77"
         ;;
@@ -130,7 +130,7 @@ if [ -z "$mode" ]; then
     done
 fi
 
-# Dump the version and exist if we're in testing mode.
+# Dump the version and exit if we're in testing mode.
 if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
     echo "$mode"
     exit
@@ -175,32 +175,44 @@ while [ -n "$1" ]; do
             ;;
         -Wl,*)
             arg="${1#-Wl,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath ]]; then
+            # 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
+                if [[ $arg != '-Wl,'* ]]; then
                     die "-Wl,-rpath was not followed by -Wl,*"
                 fi
-                rpaths+=("${arg#-Wl,}")
+                arg="${arg#-Wl,}"
+                for rpath in ${arg//,/ }; do
+                    rpaths+=("$rpath")
+                done
             else
                 other_args+=("-Wl,$arg")
             fi
             ;;
-        -Xlinker,*)
-            arg="${1#-Xlinker,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
+        -Xlinker)
+            shift; arg="$1";
+            if [[ $arg = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath ]]; then
+            elif [[ $arg = -rpath ]]; then
                 shift; arg="$1"
-                if [[ "$arg" != -Xlinker,* ]]; then
-                    die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                if [[ $arg != -Xlinker ]]; then
+                    die "-Xlinker -rpath was not followed by -Xlinker <arg>"
                 fi
-                rpaths+=("${arg#-Xlinker,}")
+                shift; arg="$1"
+                rpaths+=("$arg")
             else
-                other_args+=("-Xlinker,$arg")
+                other_args+=("-Xlinker")
+                other_args+=("$arg")
             fi
             ;;
         *)
diff --git a/lib/spack/env/pgi/case-insensitive/pgCC b/lib/spack/env/pgi/case-insensitive/pgCC
deleted file mode 120000
index e2deb67f3b..0000000000
--- a/lib/spack/env/pgi/case-insensitive/pgCC
+++ /dev/null
@@ -1 +0,0 @@
-../../cc
\ No newline at end of file
diff --git a/lib/spack/env/pgi/pgf77 b/lib/spack/env/pgi/pgc++
index 82c2b8e90a..82c2b8e90a 120000
--- a/lib/spack/env/pgi/pgf77
+++ b/lib/spack/env/pgi/pgc++
diff --git a/lib/spack/env/pgi/pgf90 b/lib/spack/env/pgi/pgfortran
index 82c2b8e90a..82c2b8e90a 120000
--- a/lib/spack/env/pgi/pgf90
+++ b/lib/spack/env/pgi/pgfortran
diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 24cfbfde71..c4665c284c 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -25,7 +25,9 @@
 __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']
+           'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
+           'set_executable', 'copy_mode', 'unset_executable_mode',
+           'remove_dead_links', 'remove_linked_tree']
 
 import os
 import sys
@@ -152,15 +154,28 @@ def set_install_permissions(path):
 def copy_mode(src, dest):
     src_mode = os.stat(src).st_mode
     dest_mode = os.stat(dest).st_mode
-    if src_mode | stat.S_IXUSR: dest_mode |= stat.S_IXUSR
-    if src_mode | stat.S_IXGRP: dest_mode |= stat.S_IXGRP
-    if src_mode | stat.S_IXOTH: dest_mode |= stat.S_IXOTH
+    if src_mode & stat.S_IXUSR: dest_mode |= stat.S_IXUSR
+    if src_mode & stat.S_IXGRP: dest_mode |= stat.S_IXGRP
+    if src_mode & stat.S_IXOTH: dest_mode |= stat.S_IXOTH
     os.chmod(dest, dest_mode)
 
 
+def unset_executable_mode(path):
+    mode = os.stat(path).st_mode
+    mode &= ~stat.S_IXUSR
+    mode &= ~stat.S_IXGRP
+    mode &= ~stat.S_IXOTH
+    os.chmod(path, mode)
+
+
 def install(src, dest):
     """Manually install a file to a particular location."""
     tty.debug("Installing %s to %s" % (src, dest))
+
+    # Expand dsst to its eventual full path if it is a directory.
+    if os.path.isdir(dest):
+        dest = join_path(dest, os.path.basename(src))
+
     shutil.copy(src, dest)
     set_install_permissions(dest)
     copy_mode(src, dest)
@@ -235,7 +250,7 @@ def touchp(path):
 def force_symlink(src, dest):
     try:
         os.symlink(src, dest)
-    except OSError, e:
+    except OSError as e:
         os.remove(dest)
         os.symlink(src, dest)
 
@@ -339,3 +354,41 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
 
     if order == 'post':
         yield (source_path, dest_path)
+
+
+def set_executable(path):
+    st = os.stat(path)
+    os.chmod(path, st.st_mode | stat.S_IEXEC)
+
+
+def remove_dead_links(root):
+    """
+    Removes any dead link that is present in root
+
+    Args:
+        root: path where to search for dead links
+
+    """
+    for file in os.listdir(root):
+        path = join_path(root, file)
+        if os.path.islink(path):
+            real_path = os.path.realpath(path)
+            if not os.path.exists(real_path):
+                os.unlink(path)
+
+def remove_linked_tree(path):
+    """
+    Removes a directory and its contents.  If the directory is a
+    symlink, follows the link and removes the real directory before
+    removing the link.
+
+    Args:
+        path: directory to be removed
+
+    """
+    if os.path.exists(path):
+        if os.path.islink(path):
+            shutil.rmtree(os.path.realpath(path), True)
+            os.unlink(path)
+        else:
+            shutil.rmtree(path, True)
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index b2db83acb7..87fc310b5a 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -177,8 +177,6 @@ def set_module_variables_for_package(pkg, m):
     """Populate the module scope of install() with some useful functions.
        This makes things easier for package writers.
     """
-    m = pkg.module
-
     # number of jobs spack will to build with.
     jobs = multiprocessing.cpu_count()
     if not pkg.parallel:
@@ -214,6 +212,13 @@ def set_module_variables_for_package(pkg, m):
     m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE')
     m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH=%s' % ":".join(get_rpaths(pkg)))
 
+    # Put spack compiler paths in module scope.
+    link_dir = spack.build_env_path
+    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'])
+
     # Emulate some shell commands for convenience
     m.pwd          = os.getcwd
     m.cd           = os.chdir
@@ -237,9 +242,9 @@ def set_module_variables_for_package(pkg, m):
 def get_rpaths(pkg):
     """Get a list of all the rpaths for a package."""
     rpaths = [pkg.prefix.lib, pkg.prefix.lib64]
-    rpaths.extend(d.prefix.lib for d in pkg.spec.traverse(root=False)
+    rpaths.extend(d.prefix.lib for d in pkg.spec.dependencies.values()
                   if os.path.isdir(d.prefix.lib))
-    rpaths.extend(d.prefix.lib64 for d in pkg.spec.traverse(root=False)
+    rpaths.extend(d.prefix.lib64 for d in pkg.spec.dependencies.values()
                   if os.path.isdir(d.prefix.lib64))
     return rpaths
 
diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py
index b1ad89dbb8..518d2703dc 100644
--- a/lib/spack/spack/cmd/checksum.py
+++ b/lib/spack/spack/cmd/checksum.py
@@ -22,23 +22,18 @@
 # 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
 import argparse
 import hashlib
-from pprint import pprint
-from subprocess import CalledProcessError
 
 import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
-
 import spack
 import spack.cmd
 import spack.util.crypto
 from spack.stage import Stage, FailedDownloadError
 from spack.version import *
 
-description ="Checksum available versions of a package."
+description = "Checksum available versions of a package."
+
 
 def setup_parser(subparser):
     subparser.add_argument(
@@ -58,25 +53,23 @@ def get_checksums(versions, urls, **kwargs):
 
     tty.msg("Downloading...")
     hashes = []
-    for i, (url, version) in enumerate(zip(urls, versions)):
-        stage = Stage(url)
+    i = 0
+    for url, version in zip(urls, versions):
         try:
-            stage.fetch()
-            if i == 0 and first_stage_function:
-                first_stage_function(stage)
-
-            hashes.append(
-                spack.util.crypto.checksum(hashlib.md5, stage.archive_file))
-        except FailedDownloadError, e:
+            with Stage(url, keep=keep_stage) as stage:
+                stage.fetch()
+                if i == 0 and first_stage_function:
+                    first_stage_function(stage)
+
+                hashes.append((version,
+                               spack.util.crypto.checksum(hashlib.md5, stage.archive_file)))
+                i += 1
+        except FailedDownloadError as e:
             tty.msg("Failed to fetch %s" % url)
-            continue
-
-        finally:
-            if not keep_stage:
-                stage.destroy()
-
-    return zip(versions, hashes)
+        except Exception as e:
+            tty.msg('Something failed on %s, skipping.\n    (%s)' % (url, e))
 
+    return hashes
 
 
 def checksum(parser, args):
@@ -95,13 +88,13 @@ def checksum(parser, args):
     else:
         versions = pkg.fetch_remote_versions()
         if not versions:
-            tty.die("Could not fetch any versions for %s." % pkg.name)
+            tty.die("Could not fetch any versions for %s" % pkg.name)
 
     sorted_versions = sorted(versions, reverse=True)
 
-    tty.msg("Found %s versions of %s." % (len(versions), pkg.name),
+    tty.msg("Found %s versions of %s" % (len(versions), pkg.name),
             *spack.cmd.elide_list(
-            ["%-10s%s" % (v, versions[v]) for v in sorted_versions]))
+                ["%-10s%s" % (v, versions[v]) for v in sorted_versions]))
     print
     archives_to_fetch = tty.get_number(
         "How many would you like to checksum?", default=5, abort='q')
@@ -116,7 +109,7 @@ def checksum(parser, args):
         keep_stage=args.keep_stage)
 
     if not version_hashes:
-        tty.die("Could not fetch any versions for %s." % pkg.name)
+        tty.die("Could not fetch any versions for %s" % pkg.name)
 
     version_lines = ["    version('%s', '%s')" % (v, h) for v, h in version_hashes]
     tty.msg("Checksummed new versions of %s:" % pkg.name, *version_lines)
diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index 75b51f6b49..3e58e82184 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -96,7 +96,7 @@ def compiler_remove(args):
     compilers = spack.compilers.compilers_for_spec(cspec, scope=args.scope)
 
     if not compilers:
-        tty.die("No compilers match spec %s." % cspec)
+        tty.die("No compilers match spec %s" % cspec)
     elif not args.all and len(compilers) > 1:
         tty.error("Multiple compilers match spec %s. Choose one:" % cspec)
         colify(reversed(sorted([c.spec for c in compilers])), indent=4)
@@ -105,7 +105,7 @@ def compiler_remove(args):
 
     for compiler in compilers:
         spack.compilers.remove_compiler_from_config(compiler.spec, scope=args.scope)
-        tty.msg("Removed compiler %s." % compiler.spec)
+        tty.msg("Removed compiler %s" % compiler.spec)
 
 
 def compiler_info(args):
@@ -114,7 +114,7 @@ def compiler_info(args):
     compilers = spack.compilers.compilers_for_spec(cspec, scope=args.scope)
 
     if not compilers:
-        tty.error("No compilers match spec %s." % cspec)
+        tty.error("No compilers match spec %s" % cspec)
     else:
         for c in compilers:
             print str(c.spec) + ":"
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index edcea0718c..4564143f83 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -156,7 +156,7 @@ def guess_name_and_version(url, args):
     # Try to deduce name and version of the new package from the URL
     version = spack.url.parse_version(url)
     if not version:
-        tty.die("Couldn't guess a version string from %s." % url)
+        tty.die("Couldn't guess a version string from %s" % url)
 
     # Try to guess a name.  If it doesn't work, allow the user to override.
     if args.alternate_name:
@@ -189,7 +189,7 @@ def find_repository(spec, args):
         try:
             repo = Repo(repo_path)
             if spec.namespace and spec.namespace != repo.namespace:
-                tty.die("Can't create package with namespace %s in repo with namespace %s."
+                tty.die("Can't create package with namespace %s in repo with namespace %s"
                         % (spec.namespace, repo.namespace))
         except RepoError as e:
             tty.die(str(e))
@@ -222,7 +222,7 @@ 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(
@@ -252,7 +252,7 @@ def create(parser, args):
     name = spec.name  # factors out namespace, if any
     repo = find_repository(spec, args)
 
-    tty.msg("This looks like a URL for %s version %s." % (name, version))
+    tty.msg("This looks like a URL for %s version %s" % (name, version))
     tty.msg("Creating template for package %s" % name)
 
     # Fetch tarballs (prompting user if necessary)
@@ -266,7 +266,7 @@ def create(parser, args):
         keep_stage=args.keep_stage)
 
     if not ver_hash_tuples:
-        tty.die("Could not fetch any tarballs for %s." % name)
+        tty.die("Could not fetch any tarballs for %s" % name)
 
     # Prepend 'py-' to python package names, by convention.
     if guesser.build_system == 'python':
@@ -291,4 +291,4 @@ def create(parser, args):
 
     # If everything checks out, go ahead and edit.
     spack.editor(pkg_path)
-    tty.msg("Created package %s." % pkg_path)
+    tty.msg("Created package %s" % pkg_path)
diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py
index 9df53312f8..2c3a8761ab 100644
--- a/lib/spack/spack/cmd/diy.py
+++ b/lib/spack/spack/cmd/diy.py
@@ -46,6 +46,9 @@ def setup_parser(subparser):
         '--skip-patch', action='store_true',
         help="Skip patching for the DIY build.")
     subparser.add_argument(
+        '-q', '--quiet', action='store_true', dest='quiet',
+        help="Do not display verbose build output while installing.")
+    subparser.add_argument(
         'spec', nargs=argparse.REMAINDER,
         help="specs to use for install.  Must contain package AND verison.")
 
@@ -92,4 +95,5 @@ def diy(self, args):
         package.do_install(
             keep_prefix=args.keep_prefix,
             ignore_deps=args.ignore_deps,
+            verbose=not args.quiet,
             keep_stage=True)   # don't remove source dir for DIY.
diff --git a/lib/spack/spack/cmd/md5.py b/lib/spack/spack/cmd/md5.py
index ef1e4f3475..f99fc0f8c2 100644
--- a/lib/spack/spack/cmd/md5.py
+++ b/lib/spack/spack/cmd/md5.py
@@ -22,32 +22,51 @@
 # 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 hashlib
 import argparse
+import hashlib
+import os
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import *
-
 import spack.util.crypto
+from spack.stage import Stage, FailedDownloadError
+
+description = "Calculate md5 checksums for files/urls."
 
-description = "Calculate md5 checksums for files."
 
 def setup_parser(subparser):
     setup_parser.parser = subparser
     subparser.add_argument('files', nargs=argparse.REMAINDER,
                            help="Files to checksum.")
 
+
+def compute_md5_checksum(url):
+    if not os.path.isfile(url):
+        with Stage(url) as stage:
+            stage.fetch()
+            value = spack.util.crypto.checksum(hashlib.md5, stage.archive_file)
+    else:
+        value = spack.util.crypto.checksum(hashlib.md5, url)
+    return value
+
+
 def md5(parser, args):
     if not args.files:
         setup_parser.parser.print_help()
         return 1
 
-    for f in args.files:
-        if not os.path.isfile(f):
-            tty.die("Not a file: %s" % f)
-        if not can_access(f):
-            tty.die("Cannot read file: %s" % f)
+    results = []
+    for url in args.files:
+        try:
+            checksum = compute_md5_checksum(url)
+            results.append((checksum, url))
+        except FailedDownloadError as e:
+            tty.warn("Failed to fetch %s" % url)
+            tty.warn("%s" % e)
+        except IOError as e:
+            tty.warn("Error when reading %s" % url)
+            tty.warn("%s" % e)
 
-        checksum = spack.util.crypto.checksum(hashlib.md5, f)
-        print "%s  %s" % (checksum, f)
+    # Dump the MD5s at last without interleaving them with downloads
+    tty.msg("%d MD5 checksums:" % len(results))
+    for checksum, url in results:
+        print "%s  %s" % (checksum, url)
diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py
index 885483a840..fcd15a6a90 100644
--- a/lib/spack/spack/cmd/mirror.py
+++ b/lib/spack/spack/cmd/mirror.py
@@ -53,11 +53,13 @@ def setup_parser(subparser):
     create_parser.add_argument('-d', '--directory', default=None,
                                help="Directory in which to create mirror.")
     create_parser.add_argument(
-        'specs', nargs=argparse.REMAINDER, help="Specs of packages to put in mirror")
+        'specs', nargs=argparse.REMAINDER,
+        help="Specs of packages to put in mirror")
     create_parser.add_argument(
         '-f', '--file', help="File with specs of packages to put in mirror.")
     create_parser.add_argument(
-        '-D', '--dependencies', action='store_true', help="Also fetch all dependencies")
+        '-D', '--dependencies', action='store_true',
+        help="Also fetch all dependencies")
     create_parser.add_argument(
         '-o', '--one-version-per-spec', action='store_const', const=1, default=0,
         help="Only fetch one 'preferred' version per spec, not all known versions.")
@@ -74,7 +76,8 @@ def setup_parser(subparser):
         help="Configuration scope to modify.")
 
     # Remove
-    remove_parser = sp.add_parser('remove', aliases=['rm'], help=mirror_remove.__doc__)
+    remove_parser = sp.add_parser('remove', aliases=['rm'],
+                                  help=mirror_remove.__doc__)
     remove_parser.add_argument('name')
     remove_parser.add_argument(
         '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
@@ -123,7 +126,7 @@ def mirror_remove(args):
 
     old_value = mirrors.pop(name)
     spack.config.update_config('mirrors', mirrors, scope=args.scope)
-    tty.msg("Removed mirror %s with url %s." % (name, old_value))
+    tty.msg("Removed mirror %s with url %s" % (name, old_value))
 
 
 def mirror_list(args):
@@ -141,15 +144,17 @@ def mirror_list(args):
 
 
 def _read_specs_from_file(filename):
+    specs = []
     with open(filename, "r") as stream:
         for i, string in enumerate(stream):
             try:
                 s = Spec(string)
                 s.package
-                args.specs.append(s)
+                specs.append(s)
             except SpackError, e:
                 tty.die("Parse error in %s, line %d:" % (args.file, i+1),
                         ">>> " + string, str(e))
+    return specs
 
 
 def mirror_create(args):
@@ -169,6 +174,7 @@ def mirror_create(args):
         specs = [Spec(n) for n in spack.repo.all_package_names()]
         specs.sort(key=lambda s: s.format("$_$@").lower())
 
+    # If the user asked for dependencies, traverse spec DAG get them.
     if args.dependencies:
         new_specs = set()
         for spec in specs:
@@ -197,7 +203,7 @@ def mirror_create(args):
 
     verb = "updated" if existed else "created"
     tty.msg(
-        "Successfully %s mirror in %s." % (verb, directory),
+        "Successfully %s mirror in %s" % (verb, directory),
         "Archive stats:",
         "  %-4d already present"  % p,
         "  %-4d added"            % m,
diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index a5a9570eb5..1d6867c1d9 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -58,7 +58,7 @@ 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:
@@ -78,7 +78,7 @@ def module_find(mtype, spec_array):
     mt = module_types[mtype]
     mod = mt(specs[0])
     if not os.path.isfile(mod.file_name):
-        tty.die("No %s module is installed for %s." % (mtype, spec))
+        tty.die("No %s module is installed for %s" % (mtype, spec))
 
     print mod.use_name
 
@@ -94,7 +94,7 @@ def module_refresh():
             shutil.rmtree(cls.path, ignore_errors=False)
         mkdirp(cls.path)
         for spec in specs:
-            tty.debug("   Writing file for %s." % spec)
+            tty.debug("   Writing file for %s" % spec)
             cls(spec).write()
 
 
diff --git a/lib/spack/spack/cmd/patch.py b/lib/spack/spack/cmd/patch.py
index 44fc8696db..b04b402738 100644
--- a/lib/spack/spack/cmd/patch.py
+++ b/lib/spack/spack/cmd/patch.py
@@ -24,6 +24,7 @@
 ##############################################################################
 import argparse
 
+import llnl.util.tty as tty
 import spack.cmd
 import spack
 
diff --git a/lib/spack/spack/cmd/repo.py b/lib/spack/spack/cmd/repo.py
index 34c755fb67..87c782000f 100644
--- a/lib/spack/spack/cmd/repo.py
+++ b/lib/spack/spack/cmd/repo.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
@@ -74,51 +74,7 @@ def setup_parser(subparser):
 
 def repo_create(args):
     """Create a new package repository."""
-    root = canonicalize_path(args.directory)
-    namespace = args.namespace
-
-    if not args.namespace:
-        namespace = os.path.basename(root)
-
-    if not re.match(r'\w[\.\w-]*', namespace):
-        tty.die("'%s' is not a valid namespace." % namespace)
-
-    existed = False
-    if os.path.exists(root):
-        if os.path.isfile(root):
-            tty.die('File %s already exists and is not a directory' % root)
-        elif os.path.isdir(root):
-            if not os.access(root, os.R_OK | os.W_OK):
-                tty.die('Cannot create new repo in %s: cannot access directory.' % root)
-            if os.listdir(root):
-                tty.die('Cannot create new repo in %s: directory is not empty.' % root)
-        existed = True
-
-    full_path = os.path.realpath(root)
-    parent = os.path.dirname(full_path)
-    if not os.access(parent, os.R_OK | os.W_OK):
-        tty.die("Cannot create repository in %s: can't access parent!" % root)
-
-    try:
-        config_path = os.path.join(root, repo_config_name)
-        packages_path = os.path.join(root, packages_dir_name)
-
-        mkdirp(packages_path)
-        with open(config_path, 'w') as config:
-            config.write("repo:\n")
-            config.write("  namespace: '%s'\n" % namespace)
-
-    except (IOError, OSError) as e:
-        tty.die('Failed to create new repository in %s.' % root,
-                "Caused by %s: %s" % (type(e), e))
-
-        # try to clean up.
-        if existed:
-            shutil.rmtree(config_path, ignore_errors=True)
-            shutil.rmtree(packages_path, ignore_errors=True)
-        else:
-            shutil.rmtree(root, ignore_errors=True)
-
+    full_path, namespace = create_repo(args.directory, args.namespace)
     tty.msg("Created repo with namespace '%s'." % namespace)
     tty.msg("To register it with spack, run this command:",
             'spack repo add %s' % full_path)
@@ -133,11 +89,11 @@ def repo_add(args):
 
     # check if the path exists
     if not os.path.exists(canon_path):
-        tty.die("No such file or directory: '%s'." % path)
+        tty.die("No such file or directory: %s" % path)
 
     # Make sure the path is a directory.
     if not os.path.isdir(canon_path):
-        tty.die("Not a Spack repository: '%s'." % path)
+        tty.die("Not a Spack repository: %s" % path)
 
     # Make sure it's actually a spack repository by constructing it.
     repo = Repo(canon_path)
@@ -147,7 +103,7 @@ def repo_add(args):
     if not repos: repos = []
 
     if repo.root in repos or path in repos:
-        tty.die("Repository is already registered with Spack: '%s'" % path)
+        tty.die("Repository is already registered with Spack: %s" % path)
 
     repos.insert(0, canon_path)
     spack.config.update_config('repos', repos, args.scope)
@@ -166,7 +122,7 @@ def repo_remove(args):
         if canon_path == repo_canon_path:
             repos.remove(repo_path)
             spack.config.update_config('repos', repos, args.scope)
-            tty.msg("Removed repository '%s'." % repo_path)
+            tty.msg("Removed repository %s" % repo_path)
             return
 
     # If it is a namespace, remove corresponding repo
@@ -176,13 +132,13 @@ def repo_remove(args):
             if repo.namespace == path_or_namespace:
                 repos.remove(path)
                 spack.config.update_config('repos', repos, args.scope)
-                tty.msg("Removed repository '%s' with namespace %s."
+                tty.msg("Removed repository %s with namespace '%s'."
                         % (repo.root, repo.namespace))
                 return
         except RepoError as e:
             continue
 
-    tty.die("No repository with path or namespace: '%s'"
+    tty.die("No repository with path or namespace: %s"
             % path_or_namespace)
 
 
diff --git a/lib/spack/spack/cmd/test-install.py b/lib/spack/spack/cmd/test-install.py
index 74017f59fb..656873a2f0 100644
--- a/lib/spack/spack/cmd/test-install.py
+++ b/lib/spack/spack/cmd/test-install.py
@@ -37,20 +37,20 @@ from spack.build_environment import InstallError
 from spack.fetch_strategy import FetchError
 import spack.cmd
 
-description = "Treat package installations as unit tests and output formatted test results"
+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")
-    
+
     subparser.add_argument(
         'package', nargs=argparse.REMAINDER, help="spec of package to install")
 
@@ -59,10 +59,10 @@ 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:
@@ -84,25 +84,25 @@ class TestResult(object):
     PASSED = 0
     FAILED = 1
     SKIPPED = 2
-    
+
 
 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
-            
-        return ((self.name, self.version, self.hashId) == 
+
+        return ((self.name, self.version, self.hashId) ==
             (other.name, other.version, other.hashId))
 
 
@@ -114,12 +114,12 @@ def fetch_log(path):
 
 
 def failed_dependencies(spec):
-    return set(childSpec for childSpec in spec.dependencies.itervalues() if not 
+    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 
+    # 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:
@@ -143,12 +143,12 @@ def create_test_output(topSpec, newInstalls, output, getLogFunc=fetch_log):
                 re.search('error:', line, re.IGNORECASE))
             errOutput = errMessages if errMessages else lines[-10:]
             errOutput = '\n'.join(itertools.chain(
-                    [spec.to_yaml(), "Errors:"], errOutput, 
+                    [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)
 
@@ -163,18 +163,18 @@ def test_install(parser, args):
 
     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")
@@ -183,7 +183,7 @@ def test_install(parser, args):
         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
@@ -202,7 +202,7 @@ def test_install(parser, args):
                 pass
             except FetchError:
                 pass
-   
+
     jrf = JunitResultFormat()
     handled = {}
     create_test_output(topSpec, newInstalls, jrf)
diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index 12c02e0ea2..d38c0b00b1 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -256,12 +256,12 @@ class Compiler(object):
 
 
     def __repr__(self):
-        """Return a string represntation of the compiler toolchain."""
+        """Return a string representation of the compiler toolchain."""
         return self.__str__()
 
 
     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))))
 
diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py
index 6159ef576c..3a04bc2ebc 100644
--- a/lib/spack/spack/compilers/__init__.py
+++ b/lib/spack/spack/compilers/__init__.py
@@ -74,28 +74,36 @@ def _to_dict(compiler):
 def get_compiler_config(arch=None, scope=None):
     """Return the compiler configuration for the specified architecture.
     """
-    # If any configuration file has compilers, just stick with the
-    # ones already configured.
-    config = spack.config.get_config('compilers', scope=scope)
-
+    # Check whether we're on a front-end (native) architecture.
     my_arch = spack.architecture.sys_type()
     if arch is None:
         arch = my_arch
 
-    if arch in config:
-        return config[arch]
-
-    # Only for the current arch in *highest* scope: automatically try to
-    # find compilers if none are configured yet.
-    if arch == my_arch and scope == 'user':
+    def init_compiler_config():
+        """Compiler search used when Spack has no compilers."""
         config[arch] = {}
         compilers = find_compilers(*get_path('PATH'))
         for compiler in compilers:
             config[arch].update(_to_dict(compiler))
         spack.config.update_config('compilers', config, scope=scope)
-        return config[arch]
 
-    return {}
+    config = spack.config.get_config('compilers', scope=scope)
+
+    # Update the configuration if there are currently no compilers
+    # configured.  Avoid updating automatically if there ARE site
+    # compilers configured but no user ones.
+    if arch == my_arch and arch not in config:
+        if scope is None:
+            # We know no compilers were configured in any scope.
+            init_compiler_config()
+        elif scope == 'user':
+            # Check the site config and update the user config if
+            # nothing is configured at the site level.
+            site_config = spack.config.get_config('compilers', scope='site')
+            if not site_config:
+                init_compiler_config()
+
+    return config[arch] if arch in config else {}
 
 
 def add_compilers_to_config(compilers, arch=None, scope=None):
diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py
index 340051019c..e406d86a24 100644
--- a/lib/spack/spack/compilers/clang.py
+++ b/lib/spack/spack/compilers/clang.py
@@ -22,7 +22,10 @@
 # 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 *
 
 class Clang(Compiler):
     # Subclasses use possible names of C compiler
@@ -47,11 +50,34 @@ class Clang(Compiler):
     @classmethod
     def default_version(self, comp):
         """The '--version' option works for clang compilers.
-           Output looks like this::
+           On most platforms, output looks like this::
 
                clang version 3.1 (trunk 149096)
                Target: x86_64-unknown-linux-gnu
                Thread model: posix
+
+          On Mac OS X, it looks like this:
+
+               Apple LLVM version 7.0.2 (clang-700.1.81)
+               Target: x86_64-apple-darwin15.2.0
+               Thread model: posix
+
         """
-        return get_compiler_version(
-            comp, '--version', r'(?:clang version|based on LLVM) ([^ )]+)')
+        if comp not in cpr._version_cache:
+            compiler = Executable(comp)
+            output = compiler('--version', output=str, error=str)
+
+            ver = 'unknown'
+            match = re.search(r'^Apple LLVM version ([^ )]+)', output)
+            if match:
+                # Apple's LLVM compiler has its own versions, so suffix them.
+                ver = match.group(1) + '-apple'
+            else:
+                # Normal clang compiler versions are left as-is
+                match = re.search(r'^clang version ([^ )]+)', output)
+                if match:
+                    ver = match.group(1)
+
+            cpr._version_cache[comp] = ver
+
+        return cpr._version_cache[comp]
diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py
index f1cc6be0d5..527a05a090 100644
--- a/lib/spack/spack/compilers/nag.py
+++ b/lib/spack/spack/compilers/nag.py
@@ -16,7 +16,7 @@ class Nag(Compiler):
     # Named wrapper links within spack.build_env_path
     link_paths = { # Use default wrappers for C and C++, in case provided in compilers.yaml
                    'cc'  : 'cc',
-                   'cxx' : 'cxx',
+                   'cxx' : 'c++',
                    'f77' : 'nag/nagfor',
                    'fc'  : 'nag/nagfor' }
 
diff --git a/lib/spack/spack/compilers/pgi.py b/lib/spack/spack/compilers/pgi.py
index 9ac74cfbdb..c6a1078bd9 100644
--- a/lib/spack/spack/compilers/pgi.py
+++ b/lib/spack/spack/compilers/pgi.py
@@ -29,28 +29,28 @@ class Pgi(Compiler):
     cc_names = ['pgcc']
 
     # Subclasses use possible names of C++ compiler
-    cxx_names = ['pgCC']
+    cxx_names = ['pgc++', 'pgCC']
 
     # Subclasses use possible names of Fortran 77 compiler
-    f77_names = ['pgf77']
+    f77_names = ['pgfortran', 'pgf77']
 
     # Subclasses use possible names of Fortran 90 compiler
-    fc_names = ['pgf95', 'pgf90']
+    fc_names = ['pgfortran', 'pgf95', 'pgf90']
 
     # Named wrapper links within spack.build_env_path
     link_paths = { 'cc'  : 'pgi/pgcc',
-                   'cxx' : 'pgi/case-insensitive/pgCC',
-                   'f77' : 'pgi/pgf77',
-                   'fc'  : 'pgi/pgf90' }
+                   'cxx' : 'pgi/pgc++',
+                   'f77' : 'pgi/pgfortran',
+                   'fc'  : 'pgi/pgfortran' }
 
     @classmethod
     def default_version(cls, comp):
         """The '-V' option works for all the PGI compilers.
            Output looks like this::
 
-               pgf95 10.2-0 64-bit target on x86-64 Linux -tp nehalem-64
-               Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
-               Copyright 2000-2010, STMicroelectronics, Inc.  All Rights Reserved.
+               pgcc 15.10-0 64-bit target on x86-64 Linux -tp sandybridge
+               The Portland Group - PGI Compilers and Tools
+               Copyright (c) 2015, NVIDIA CORPORATION.  All rights reserved.
         """
         return get_compiler_version(
             comp, '-V', r'pg[^ ]* ([^ ]+) \d\d\d?-bit target')
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 71900282f5..807a898644 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -239,7 +239,7 @@ config_scopes = OrderedDict()
 def validate_section_name(section):
     """Raise a ValueError if the section is not a valid section."""
     if section not in section_schemas:
-        raise ValueError("Invalid config section: '%s'.  Options are %s."
+        raise ValueError("Invalid config section: '%s'.  Options are %s"
                          % (section, section_schemas))
 
 
@@ -369,7 +369,7 @@ def validate_scope(scope):
         return config_scopes[scope]
 
     else:
-        raise ValueError("Invalid config scope: '%s'.  Must be one of %s."
+        raise ValueError("Invalid config scope: '%s'.  Must be one of %s"
                          % (scope, config_scopes.keys()))
 
 
@@ -384,7 +384,7 @@ def _read_config_file(filename, schema):
             "Invlaid 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)
+        raise ConfigFileError("Config file is not readable: %s" % filename)
 
     try:
         tty.debug("Reading config file %s" % filename)
diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index 9cbe7de44a..089d29325e 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -330,7 +330,7 @@ class Database(object):
             found = rec.ref_count
             if not expected == found:
                 raise AssertionError(
-                    "Invalid ref_count: %s: %d (expected %d), in DB %s."
+                    "Invalid ref_count: %s: %d (expected %d), in DB %s"
                     % (key, found, expected, self._index_path))
 
 
diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py
index 0b98211cb9..61cd303012 100644
--- a/lib/spack/spack/directives.py
+++ b/lib/spack/spack/directives.py
@@ -125,7 +125,7 @@ class directive(object):
             dicts = (dicts,)
         elif type(dicts) not in (list, tuple):
             raise TypeError(
-                "dicts arg must be list, tuple, or string. Found %s."
+                "dicts arg must be list, tuple, or string. Found %s"
                 % type(dicts))
 
         self.dicts = dicts
@@ -174,7 +174,11 @@ def version(pkg, ver, checksum=None, **kwargs):
 
 
 def _depends_on(pkg, spec, when=None):
-    if when is None:
+    # If when is False do nothing
+    if when is False:
+        return
+    # If when is None or True make sure the condition is always satisfied
+    if when is None or when is True:
         when = pkg.name
     when_spec = parse_anonymous_spec(when, pkg.name)
 
@@ -296,8 +300,8 @@ def resource(pkg, **kwargs):
         raise RuntimeError(message)
     when_spec = parse_anonymous_spec(when, pkg.name)
     resources = pkg.resources.setdefault(when_spec, [])
-    fetcher = from_kwargs(**kwargs)
     name = kwargs.get('name')
+    fetcher = from_kwargs(**kwargs)
     resources.append(Resource(name, fetcher, destination, placement))
 
 
@@ -313,5 +317,5 @@ class CircularReferenceError(DirectiveError):
     def __init__(self, directive, package):
         super(CircularReferenceError, self).__init__(
             directive,
-            "Package '%s' cannot pass itself to %s." % (package, directive))
+            "Package '%s' cannot pass itself to %s" % (package, directive))
         self.package = package
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index d5b61ee7f0..b94468faf0 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -85,6 +85,16 @@ class DirectoryLayout(object):
         raise NotImplementedError()
 
 
+    def check_installed(self, spec):
+        """Checks whether a spec is installed.
+
+        Return the spec's prefix, if it is installed, None otherwise.
+
+        Raise an exception if the install is inconsistent or corrupt.
+        """
+        raise NotImplementedError()
+
+
     def extension_map(self, spec):
         """Get a dict of currently installed extension packages for a spec.
 
@@ -173,7 +183,9 @@ class YamlDirectoryLayout(DirectoryLayout):
 
         self.spec_file_name      = 'spec.yaml'
         self.extension_file_name = 'extensions.yaml'
-        self.build_log_name      = 'build.out' # TODO: use config file.
+        self.build_log_name      = 'build.out'  # build log.
+        self.build_env_name      = 'build.env'  # build environment
+        self.packages_dir        = 'repos'      # archive of package.py files
 
         # Cache of already written/read extension maps.
         self._extension_maps = {}
@@ -239,29 +251,49 @@ class YamlDirectoryLayout(DirectoryLayout):
                          self.build_log_name)
 
 
+    def build_env_path(self, spec):
+        return join_path(self.path_for_spec(spec), self.metadata_dir,
+                         self.build_env_name)
+
+
+    def build_packages_path(self, spec):
+        return join_path(self.path_for_spec(spec), self.metadata_dir,
+                         self.packages_dir)
+
+
     def create_install_directory(self, spec):
         _check_concrete(spec)
 
+        prefix = self.check_installed(spec)
+        if prefix:
+            raise InstallDirectoryAlreadyExistsError(prefix)
+
+        mkdirp(self.metadata_path(spec))
+        self.write_spec(spec, self.spec_file_path(spec))
+
+
+    def check_installed(self, spec):
+        _check_concrete(spec)
         path = self.path_for_spec(spec)
         spec_file_path = self.spec_file_path(spec)
 
-        if os.path.isdir(path):
-            if not os.path.isfile(spec_file_path):
-                raise InconsistentInstallDirectoryError(
-                    'No spec file found at path %s' % spec_file_path)
+        if not os.path.isdir(path):
+            return None
 
-            installed_spec = self.read_spec(spec_file_path)
-            if installed_spec == self.spec:
-                raise InstallDirectoryAlreadyExistsError(path)
+        if not os.path.isfile(spec_file_path):
+            raise InconsistentInstallDirectoryError(
+                'Inconsistent state: install prefix exists but contains no spec.yaml:',
+                "  " + path)
 
-            if spec.dag_hash() == installed_spec.dag_hash():
-                raise SpecHashCollisionError(installed_hash, spec_hash)
-            else:
-                raise InconsistentInstallDirectoryError(
-                    'Spec file in %s does not match hash!' % spec_file_path)
+        installed_spec = self.read_spec(spec_file_path)
+        if installed_spec == spec:
+            return path
 
-        mkdirp(self.metadata_path(spec))
-        self.write_spec(spec, spec_file_path)
+        if spec.dag_hash() == installed_spec.dag_hash():
+            raise SpecHashCollisionError(installed_hash, spec_hash)
+        else:
+            raise InconsistentInstallDirectoryError(
+                'Spec file in %s does not match hash!' % spec_file_path)
 
 
     def all_specs(self):
@@ -331,7 +363,7 @@ class YamlDirectoryLayout(DirectoryLayout):
 
                         if not dag_hash in by_hash:
                             raise InvalidExtensionSpecError(
-                                "Spec %s not found in %s." % (dag_hash, prefix))
+                                "Spec %s not found in %s" % (dag_hash, prefix))
 
                         ext_spec = by_hash[dag_hash]
                         if not prefix == ext_spec.prefix:
@@ -395,8 +427,8 @@ class YamlDirectoryLayout(DirectoryLayout):
 
 class DirectoryLayoutError(SpackError):
     """Superclass for directory layout errors."""
-    def __init__(self, message):
-        super(DirectoryLayoutError, self).__init__(message)
+    def __init__(self, message, long_msg=None):
+        super(DirectoryLayoutError, self).__init__(message, long_msg)
 
 
 class SpecHashCollisionError(DirectoryLayoutError):
@@ -418,8 +450,8 @@ class RemoveFailedError(DirectoryLayoutError):
 
 class InconsistentInstallDirectoryError(DirectoryLayoutError):
     """Raised when a package seems to be installed to the wrong place."""
-    def __init__(self, message):
-        super(InconsistentInstallDirectoryError, self).__init__(message)
+    def __init__(self, message, long_msg=None):
+        super(InconsistentInstallDirectoryError, self).__init__(message, long_msg)
 
 
 class InstallDirectoryAlreadyExistsError(DirectoryLayoutError):
@@ -446,7 +478,7 @@ class ExtensionConflictError(DirectoryLayoutError):
     """Raised when an extension is added to a package that already has it."""
     def __init__(self, spec, ext_spec, conflict):
         super(ExtensionConflictError, self).__init__(
-            "%s cannot be installed in %s because it conflicts with %s."% (
+            "%s cannot be installed in %s because it conflicts with %s"% (
                 ext_spec.short_spec, spec.short_spec, conflict.short_spec))
 
 
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 337dd1e198..0d0a7db8a9 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -44,6 +44,7 @@ import os
 import sys
 import re
 import shutil
+import copy
 from functools import wraps
 import llnl.util.tty as tty
 from llnl.util.filesystem import *
@@ -55,23 +56,28 @@ from spack.util.string import *
 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 = []
 
+
 def _needs_stage(fun):
     """Many methods on fetch strategies require a stage to be set
        using set_stage().  This decorator adds a check for self.stage."""
+
     @wraps(fun)
     def wrapper(self, *args, **kwargs):
         if not self.stage:
             raise NoStageError(fun)
         return fun(self, *args, **kwargs)
+
     return wrapper
 
 
 class FetchStrategy(object):
     """Superclass of all fetch strategies."""
-    enabled = False             # Non-abstract subclasses should be enabled.
+    enabled = False  # Non-abstract subclasses should be enabled.
     required_attributes = None  # Attributes required in version() args.
 
     class __metaclass__(type):
@@ -80,28 +86,28 @@ class FetchStrategy(object):
             type.__init__(cls, name, bases, dict)
             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.
         self.stage = None
 
-
     def set_stage(self, stage):
         """This is called by Stage before any of the fetching
            methods are called on the stage."""
         self.stage = stage
 
-
     # Subclasses need to implement these methods
     def fetch(self):   pass  # Return True on success, False on fail.
+
     def check(self):   pass  # Do checksum.
+
     def expand(self):  pass  # Expand archive.
+
     def reset(self):   pass  # Revert to freshly downloaded state.
 
     def archive(self, destination): pass  # Used to create tarball for mirror.
 
-    def __str__(self):       # Should be human readable URL.
+    def __str__(self):  # Should be human readable URL.
         return "FetchStrategy.__str___"
 
     # This method is used to match fetch strategies to version()
@@ -111,6 +117,15 @@ class FetchStrategy(object):
         return any(k in args for k in cls.required_attributes)
 
 
+@pattern.composite(interface=FetchStrategy)
+class FetchStrategyComposite(object):
+    """
+    Composite for a FetchStrategy object. Implements the GoF composite pattern.
+    """
+    matches = FetchStrategy.matches
+    set_stage = FetchStrategy.set_stage
+
+
 class URLFetchStrategy(FetchStrategy):
     """FetchStrategy that pulls source code from a URL for an archive,
        checks the archive against a checksum,and decompresses the archive.
@@ -129,6 +144,8 @@ class URLFetchStrategy(FetchStrategy):
         self.digest = kwargs.get('md5', None)
         if not self.digest: self.digest = digest
 
+        self.expand_archive = kwargs.get('expand', True)
+
         if not self.url:
             raise ValueError("URLFetchStrategy requires a url for fetching.")
 
@@ -137,20 +154,20 @@ class URLFetchStrategy(FetchStrategy):
         self.stage.chdir()
 
         if self.archive_file:
-            tty.msg("Already downloaded %s." % self.archive_file)
+            tty.msg("Already downloaded %s" % self.archive_file)
             return
 
         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,]
+        curl_args = ['-O',  # save file to disk
+                     '-f',  # fail on >400 errors
+                     '-D', '-',  # print out HTML headers
+                     '-L', self.url, ]
 
         if sys.stdout.isatty():
             curl_args.append('-#')  # status bar when using a tty
         else:
-            curl_args.append('-sS') # just errors when not.
+            curl_args.append('-sS')  # just errors when not.
 
         # Run curl but grab the mime type from the http headers
         headers = spack.curl(
@@ -164,24 +181,23 @@ class URLFetchStrategy(FetchStrategy):
             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
@@ -196,7 +212,6 @@ class URLFetchStrategy(FetchStrategy):
         if not self.archive_file:
             raise FailedDownloadError(self.url)
 
-
     @property
     def archive_file(self):
         """Path to the source archive within this stage directory."""
@@ -204,12 +219,16 @@ class URLFetchStrategy(FetchStrategy):
 
     @_needs_stage
     def expand(self):
+        if not self.expand_archive:
+            tty.msg("Skipping expand step for %s" % self.archive_file)
+            return
+
         tty.msg("Staging archive: %s" % self.archive_file)
 
         self.stage.chdir()
         if not self.archive_file:
             raise NoArchiveFileError("URLFetchStrategy couldn't find archive file",
-                                      "Failed on expand() for URL %s" % self.url)
+                                     "Failed on expand() for URL %s" % self.url)
 
         decompress = decompressor_for(self.archive_file)
 
@@ -241,7 +260,6 @@ class URLFetchStrategy(FetchStrategy):
         # Set the wd back to the stage when done.
         self.stage.chdir()
 
-
     def archive(self, destination):
         """Just moves this archive to the destination."""
         if not self.archive_file:
@@ -252,7 +270,6 @@ class URLFetchStrategy(FetchStrategy):
 
         shutil.move(self.archive_file, destination)
 
-
     @_needs_stage
     def check(self):
         """Check the downloaded archive against a checksum digest.
@@ -263,9 +280,8 @@ class URLFetchStrategy(FetchStrategy):
         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):
@@ -277,12 +293,10 @@ class URLFetchStrategy(FetchStrategy):
             shutil.rmtree(self.stage.source_path, ignore_errors=True)
         self.expand()
 
-
     def __repr__(self):
         url = self.url if self.url else "no url"
         return "URLFetchStrategy<%s>" % url
 
-
     def __str__(self):
         if self.url:
             return self.url
@@ -298,33 +312,30 @@ 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(
-            "%s requires %s argument." % (self.__class__, name))
+                "%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:
             setattr(self, rt, kwargs.get(rt, None))
 
-
     @_needs_stage
     def check(self):
-        tty.msg("No checksum needed when fetching with %s." % self.name)
-
+        tty.msg("No checksum needed when fetching with %s" % self.name)
 
     @_needs_stage
     def expand(self):
         tty.debug("Source fetched with %s is already expanded." % self.name)
 
-
     @_needs_stage
     def archive(self, destination, **kwargs):
-        assert(extension(destination) == 'tar.gz')
-        assert(self.stage.source_path.startswith(self.stage.path))
+        assert (extension(destination) == 'tar.gz')
+        assert (self.stage.source_path.startswith(self.stage.path))
 
         tar = which('tar', required=True)
 
@@ -338,16 +349,13 @@ class VCSFetchStrategy(FetchStrategy):
         self.stage.chdir()
         tar('-czf', destination, os.path.basename(self.stage.source_path))
 
-
     def __str__(self):
         return "VCS: %s" % self.url
 
-
     def __repr__(self):
         return "%s<%s>" % (self.__class__, self.url)
 
 
-
 class GitFetchStrategy(VCSFetchStrategy):
     """Fetch strategy that gets source code from a git repository.
        Use like this in a package:
@@ -368,30 +376,31 @@ class GitFetchStrategy(VCSFetchStrategy):
     required_attributes = ('git',)
 
     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(GitFetchStrategy, self).__init__(
-            'git', 'tag', 'branch', 'commit', **kwargs)
+                'git', 'tag', 'branch', 'commit', **forwarded_args)
         self._git = None
 
-
     @property
     def git_version(self):
         vstring = self.git('--version', output=str).lstrip('git version ')
         return Version(vstring)
 
-
     @property
     def git(self):
         if not self._git:
             self._git = which('git', required=True)
         return self._git
 
-
     @_needs_stage
     def fetch(self):
         self.stage.chdir()
 
         if self.stage.source_path:
-            tty.msg("Already fetched %s." % self.stage.source_path)
+            tty.msg("Already fetched %s" % self.stage.source_path)
             return
 
         args = []
@@ -418,7 +427,7 @@ class GitFetchStrategy(VCSFetchStrategy):
             if self.branch:
                 args.extend(['--branch', self.branch])
             elif self.tag and self.git_version >= ver('1.8.5.2'):
-                    args.extend(['--branch', self.tag])
+                args.extend(['--branch', self.tag])
 
             # Try to be efficient if we're using a new enough git.
             # This checks out only one branch's history
@@ -429,7 +438,7 @@ class GitFetchStrategy(VCSFetchStrategy):
             # Yet more efficiency, only download a 1-commit deep tree
             if self.git_version >= ver('1.7.1'):
                 try:
-                    self.git(*(args + ['--depth','1', self.url]))
+                    self.git(*(args + ['--depth', '1', self.url]))
                     cloned = True
                 except spack.error.SpackError:
                     # This will fail with the dumb HTTP transport
@@ -452,18 +461,15 @@ class GitFetchStrategy(VCSFetchStrategy):
                 self.git('pull', '--tags', ignore_errors=1)
                 self.git('checkout', self.tag)
 
-
     def archive(self, destination):
         super(GitFetchStrategy, self).archive(destination, exclude='.git')
 
-
     @_needs_stage
     def reset(self):
         self.stage.chdir_to_source()
         self.git('checkout', '.')
         self.git('clean', '-f')
 
-
     def __str__(self):
         return "[git] %s" % self.url
 
@@ -483,26 +489,28 @@ class SvnFetchStrategy(VCSFetchStrategy):
     required_attributes = ['svn']
 
     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(SvnFetchStrategy, self).__init__(
-            'svn', 'revision', **kwargs)
+                'svn', 'revision', **forwarded_args)
         self._svn = None
         if self.revision is not None:
             self.revision = str(self.revision)
 
-
     @property
     def svn(self):
         if not self._svn:
             self._svn = which('svn', required=True)
         return self._svn
 
-
     @_needs_stage
     def fetch(self):
         self.stage.chdir()
 
         if self.stage.source_path:
-            tty.msg("Already fetched %s." % self.stage.source_path)
+            tty.msg("Already fetched %s" % self.stage.source_path)
             return
 
         tty.msg("Trying to check out svn repository: %s" % self.url)
@@ -515,7 +523,6 @@ class SvnFetchStrategy(VCSFetchStrategy):
         self.svn(*args)
         self.stage.chdir_to_source()
 
-
     def _remove_untracked_files(self):
         """Removes untracked files in an svn repository."""
         status = self.svn('status', '--no-ignore', output=str)
@@ -529,23 +536,19 @@ class SvnFetchStrategy(VCSFetchStrategy):
             elif os.path.isdir(path):
                 shutil.rmtree(path, ignore_errors=True)
 
-
     def archive(self, destination):
         super(SvnFetchStrategy, self).archive(destination, exclude='.svn')
 
-
     @_needs_stage
     def reset(self):
         self.stage.chdir_to_source()
         self._remove_untracked_files()
         self.svn('revert', '.', '-R')
 
-
     def __str__(self):
         return "[svn] %s" % self.url
 
 
-
 class HgFetchStrategy(VCSFetchStrategy):
     """Fetch strategy that gets source code from a Mercurial repository.
        Use like this in a package:
@@ -567,11 +570,14 @@ class HgFetchStrategy(VCSFetchStrategy):
     required_attributes = ['hg']
 
     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(HgFetchStrategy, self).__init__(
-            'hg', 'revision', **kwargs)
+                'hg', 'revision', **forwarded_args)
         self._hg = None
 
-
     @property
     def hg(self):
         if not self._hg:
@@ -583,7 +589,7 @@ class HgFetchStrategy(VCSFetchStrategy):
         self.stage.chdir()
 
         if self.stage.source_path:
-            tty.msg("Already fetched %s." % self.stage.source_path)
+            tty.msg("Already fetched %s" % self.stage.source_path)
             return
 
         args = []
@@ -597,11 +603,9 @@ class HgFetchStrategy(VCSFetchStrategy):
 
         self.hg(*args)
 
-
     def archive(self, destination):
         super(HgFetchStrategy, self).archive(destination, exclude='.hg')
 
-
     @_needs_stage
     def reset(self):
         self.stage.chdir()
@@ -619,7 +623,6 @@ class HgFetchStrategy(VCSFetchStrategy):
         shutil.move(scrubbed, source_path)
         self.stage.chdir_to_source()
 
-
     def __str__(self):
         return "[hg] %s" % self.url
 
@@ -693,9 +696,10 @@ class FetchError(spack.error.SpackError):
 
 class FailedDownloadError(FetchError):
     """Raised wen a download fails."""
+
     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
 
 
@@ -718,12 +722,14 @@ class InvalidArgsError(FetchError):
 
 class ChecksumError(FetchError):
     """Raised when archive fails to checksum."""
+
     def __init__(self, message, long_msg=None):
         super(ChecksumError, self).__init__(message, long_msg)
 
 
 class NoStageError(FetchError):
     """Raised when fetch operations are called before set_stage()."""
+
     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/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py
new file mode 100644
index 0000000000..3390ecea29
--- /dev/null
+++ b/lib/spack/spack/hooks/sbang.py
@@ -0,0 +1,77 @@
+##############################################################################
+# Copyright (c) 2013-2015, 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 os
+
+from llnl.util.filesystem import *
+import llnl.util.tty as tty
+
+import spack
+import spack.modules
+
+# Character limit for shebang line.  Using Linux's 127 characters
+# here, as it is the shortest I could find on a modern OS.
+shebang_limit = 127
+
+def shebang_too_long(path):
+    """Detects whether an file has a shebang line that is too long."""
+    with open(path, 'r') as script:
+        bytes = script.read(2)
+        if bytes != '#!':
+            return False
+
+        line = bytes + script.readline()
+        return len(line) > shebang_limit
+
+
+def filter_shebang(path):
+    """Adds a second shebang line, using sbang, at the beginning of a file."""
+    backup = path + ".shebang.bak"
+    os.rename(path, backup)
+
+    with open(backup, 'r') as bak_file:
+        original = bak_file.read()
+
+    with open(path, 'w') as new_file:
+        new_file.write('#!/bin/bash %s/bin/sbang\n' % spack.spack_root)
+        new_file.write(original)
+
+    copy_mode(backup, path)
+    unset_executable_mode(backup)
+
+    tty.warn("Patched overly long shebang in %s" % path)
+
+
+def post_install(pkg):
+    """This hook edits scripts so that they call /bin/bash
+       $spack_prefix/bin/sbang instead of something longer than the
+       shebang limit."""
+    if not os.path.isdir(pkg.prefix.bin):
+        return
+
+    for file in os.listdir(pkg.prefix.bin):
+        path = os.path.join(pkg.prefix.bin, file)
+        if shebang_too_long(path):
+            filter_shebang(path)
+
diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py
index 1d9b0e7ef2..6981f69ac0 100644
--- a/lib/spack/spack/mirror.py
+++ b/lib/spack/spack/mirror.py
@@ -45,25 +45,31 @@ from spack.version import *
 from spack.util.compression import extension, allowed_archive
 
 
-def mirror_archive_filename(spec):
+def mirror_archive_filename(spec, fetcher):
     """Get the name of the spec's archive in the mirror."""
     if not spec.version.concrete:
         raise ValueError("mirror.path requires spec with concrete version.")
 
-    fetcher = spec.package.fetcher
     if isinstance(fetcher, fs.URLFetchStrategy):
-        # If we fetch this version with a URLFetchStrategy, use URL's archive type
-        ext = url.downloaded_file_extension(fetcher.url)
+        if fetcher.expand_archive:
+            # If we fetch this version with a URLFetchStrategy, use URL's archive type
+            ext = url.downloaded_file_extension(fetcher.url)
+        else:
+            # If the archive shouldn't be expanded, don't check for its extension.
+            ext = None
     else:
         # Otherwise we'll make a .tar.gz ourselves
         ext = 'tar.gz'
 
-    return "%s-%s.%s" % (spec.package.name, spec.version, ext)
+    filename = "%s-%s" % (spec.package.name, spec.version)
+    if ext:
+        filename += ".%s" % ext
+    return filename
 
 
-def mirror_archive_path(spec):
+def mirror_archive_path(spec, fetcher):
     """Get the relative path to the spec's archive within a mirror."""
-    return join_path(spec.name, mirror_archive_filename(spec))
+    return join_path(spec.name, mirror_archive_filename(spec, fetcher))
 
 
 def get_matching_versions(specs, **kwargs):
@@ -74,10 +80,11 @@ def get_matching_versions(specs, **kwargs):
 
         # Skip any package that has no known versions.
         if not pkg.versions:
-            tty.msg("No safe (checksummed) versions for package %s." % pkg.name)
+            tty.msg("No safe (checksummed) versions for package %s" % pkg.name)
             continue
 
         num_versions = kwargs.get('num_versions', 0)
+        matching_spec = []
         for i, v in enumerate(reversed(sorted(pkg.versions))):
             # Generate no more than num_versions versions for each spec.
             if num_versions and i >= num_versions:
@@ -88,7 +95,11 @@ def get_matching_versions(specs, **kwargs):
                 s = Spec(pkg.name)
                 s.versions = VersionList([v])
                 s.variants = spec.variants.copy()
-                matching.append(s)
+                matching_spec.append(s)
+
+        if not matching_spec:
+            tty.warn("No known version matches spec: %s" % spec)
+        matching.extend(matching_spec)
 
     return matching
 
@@ -106,7 +117,6 @@ def suggest_archive_basename(resource):
     return basename
 
 
-
 def create(path, specs, **kwargs):
     """Create a directory to be used as a spack mirror, and fill it with
        package archives.
@@ -147,81 +157,72 @@ def create(path, specs, **kwargs):
     # Get the absolute path of the root before we start jumping around.
     mirror_root = os.path.abspath(path)
     if not os.path.isdir(mirror_root):
-        mkdirp(mirror_root)
+        try:
+            mkdirp(mirror_root)
+        except OSError as e:
+            raise MirrorError(
+                "Cannot create directory '%s':" % mirror_root, str(e))
 
     # Things to keep track of while parsing specs.
-    present  = []
-    mirrored = []
-    error    = []
+    categories = {
+        'present': [],
+        'mirrored': [],
+        'error': []
+    }
 
     # Iterate through packages and download all the safe tarballs for each of them
-    everything_already_exists = True
     for spec in version_specs:
-        pkg = spec.package
-
-        stage = None
-        try:
-            # create a subdirectory for the current package@version
-            archive_path = os.path.abspath(join_path(mirror_root, mirror_archive_path(spec)))
-            subdir = os.path.dirname(archive_path)
-            mkdirp(subdir)
-
-            if os.path.exists(archive_path):
-                tty.msg("Already added %s" % spec.format("$_$@"))
-            else:
-                everything_already_exists = False
-                # Set up a stage and a fetcher for the download
-                unique_fetch_name = spec.format("$_$@")
-                fetcher = fs.for_package_version(pkg, pkg.version)
-                stage = Stage(fetcher, name=unique_fetch_name)
-                fetcher.set_stage(stage)
-
-                # Do the fetch and checksum if necessary
-                fetcher.fetch()
-                if not kwargs.get('no_checksum', False):
-                    fetcher.check()
-                    tty.msg("Checksum passed for %s@%s" % (pkg.name, pkg.version))
-
-                # Fetchers have to know how to archive their files.  Use
-                # that to move/copy/create an archive in the mirror.
-                fetcher.archive(archive_path)
-                tty.msg("Added %s." % spec.format("$_$@"))
-
-            # Fetch resources if they are associated with the spec
-            resources = pkg._get_resources()
-            for resource in resources:
-                resource_archive_path = join_path(subdir, suggest_archive_basename(resource))
-                if os.path.exists(resource_archive_path):
-                    tty.msg("Already added resource %s (%s@%s)." % (resource.name, pkg.name, pkg.version))
-                    continue
-                everything_already_exists = False
-                resource_stage_folder = pkg._resource_stage(resource)
-                resource_stage = Stage(resource.fetcher, name=resource_stage_folder)
-                resource.fetcher.set_stage(resource_stage)
-                resource.fetcher.fetch()
-                if not kwargs.get('no_checksum', False):
-                    resource.fetcher.check()
-                    tty.msg("Checksum passed for the resource %s (%s@%s)" % (resource.name, pkg.name, pkg.version))
-                resource.fetcher.archive(resource_archive_path)
-                tty.msg("Added resource %s (%s@%s)." % (resource.name, pkg.name, pkg.version))
-
-            if everything_already_exists:
-                present.append(spec)
-            else:
-                mirrored.append(spec)
-
-        except Exception, e:
-            if spack.debug:
-                sys.excepthook(*sys.exc_info())
-            else:
-                tty.warn("Error while fetching %s." % spec.format('$_$@'), e.message)
-            error.append(spec)
-
-        finally:
-            if stage:
-                stage.destroy()
-
-    return (present, mirrored, error)
+        add_single_spec(spec, mirror_root, categories, **kwargs)
+
+    return categories['present'], categories['mirrored'], categories['error']
+
+
+def add_single_spec(spec, mirror_root, categories, **kwargs):
+    tty.msg("Adding package {pkg} to mirror".format(pkg=spec.format("$_$@")))
+    spec_exists_in_mirror = True
+    try:
+        with spec.package.stage:
+            # fetcher = stage.fetcher
+            # fetcher.fetch()
+            # ...
+            # fetcher.archive(archive_path)
+            for ii, stage in enumerate(spec.package.stage):
+                fetcher = stage.fetcher
+                if ii == 0:
+                    # create a subdirectory for the current package@version
+                    archive_path = os.path.abspath(join_path(mirror_root, mirror_archive_path(spec, fetcher)))
+                    name = spec.format("$_$@")
+                else:
+                    resource = stage.resource
+                    archive_path = join_path(subdir, suggest_archive_basename(resource))
+                    name = "{resource} ({pkg}).".format(resource=resource.name, pkg=spec.format("$_$@"))
+                subdir = os.path.dirname(archive_path)
+                mkdirp(subdir)
+
+                if os.path.exists(archive_path):
+                    tty.msg("{name} : already added".format(name=name))
+                else:
+                    spec_exists_in_mirror = False
+                    fetcher.fetch()
+                    if not kwargs.get('no_checksum', False):
+                        fetcher.check()
+                        tty.msg("{name} : checksum passed".format(name=name))
+
+                    # Fetchers have to know how to archive their files.  Use
+                    # that to move/copy/create an archive in the mirror.
+                    fetcher.archive(archive_path)
+                    tty.msg("{name} : added".format(name=name))
+
+        if spec_exists_in_mirror:
+            categories['present'].append(spec)
+        else:
+            categories['mirrored'].append(spec)
+    except Exception as e:
+        if spack.debug:
+            sys.excepthook(*sys.exc_info())
+        else:
+            tty.warn("Error while fetching %s" % spec.format('$_$@'), e.message)
+        categories['error'].append(spec)
 
 
 class MirrorError(spack.error.SpackError):
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 7036626e29..c27043db8c 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -33,6 +33,7 @@ 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
 
@@ -121,6 +122,7 @@ class EnvModule(object):
                     ('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'))]:
 
@@ -194,12 +196,14 @@ class Dotkit(EnvModule):
     @property
     def file_name(self):
         return join_path(Dotkit.path, self.spec.architecture,
-                         self.spec.format('$_$@$%@$+$#.dk'))
+                         '%s.dk' % self.use_name)
 
     @property
     def use_name(self):
-        return self.spec.format('$_$@$%@$+$#')
-
+      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):
         # Category
@@ -235,7 +239,10 @@ class TclModule(EnvModule):
 
     @property
     def use_name(self):
-        return self.spec.format('$_$@$%@$+$#')
+      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, m_file):
diff --git a/lib/spack/spack/multimethod.py b/lib/spack/spack/multimethod.py
index df9b9b2ab1..3cd17e796a 100644
--- a/lib/spack/spack/multimethod.py
+++ b/lib/spack/spack/multimethod.py
@@ -138,7 +138,7 @@ class when(object):
        methods like install() that depend on the package's spec.
        For example:
 
-       .. code-block::
+       .. code-block:: python
 
           class SomePackage(Package):
               ...
@@ -163,26 +163,28 @@ class when(object):
        if you only have part of the install that is platform specific, you
        could do this:
 
-       class SomePackage(Package):
-           ...
-           # virtual dependence on MPI.
-           # could resolve to mpich, mpich2, OpenMPI
-           depends_on('mpi')
+       .. code-block:: python
 
-           def setup(self):
-               # do nothing in the default case
-               pass
+          class SomePackage(Package):
+              ...
+              # virtual dependence on MPI.
+              # could resolve to mpich, mpich2, OpenMPI
+              depends_on('mpi')
+
+              def setup(self):
+                  # do nothing in the default case
+                  pass
 
-           @when('^openmpi')
-           def setup(self):
-               # do something special when this is built with OpenMPI for
-               # its MPI implementations.
+              @when('^openmpi')
+              def setup(self):
+                  # do something special when this is built with OpenMPI for
+                  # its MPI implementations.
 
 
-           def install(self, prefix):
-               # Do common install stuff
-               self.setup()
-               # Do more common install stuff
+              def install(self, prefix):
+                  # Do common install stuff
+                  self.setup()
+                  # Do more common install stuff
 
        There must be one (and only one) @when clause that matches the
        package's spec.  If there is more than one, or if none match,
@@ -193,10 +195,11 @@ class when(object):
        platform-specific versions.  There's not much we can do to get
        around this because of the way decorators work.
     """
-class when(object):
     def __init__(self, spec):
         pkg = get_calling_module_name()
-        self.spec = parse_anonymous_spec(spec, pkg)
+        if spec is True:
+            spec = pkg
+        self.spec = parse_anonymous_spec(spec, pkg) if spec is not False else None
 
     def __call__(self, method):
         # Get the first definition of the method in the calling scope
@@ -207,7 +210,9 @@ class when(object):
         if not type(original_method) == SpecMultiMethod:
             original_method = SpecMultiMethod(original_method)
 
-        original_method.register(self.spec, method)
+        if self.spec is not None:
+            original_method.register(self.spec, method)
+
         return original_method
 
 
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 8dae85cf11..3dcdfc3273 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -58,14 +58,16 @@ import spack.compilers
 import spack.mirror
 import spack.hooks
 import spack.directives
+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 spack.stage import Stage
+from spack.stage import Stage, ResourceStage, StageComposite
 from spack.util.compression import allowed_archive, extension
 from spack.util.executable import ProcessError
+from spack.util.environment import dump_environment
 
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@@ -433,23 +435,51 @@ class Package(object):
         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)
+        return stage
+
+    def _make_root_stage(self, fetcher):
+        # Construct a mirror path (TODO: get this out of package.py)
+        mp = spack.mirror.mirror_archive_path(self.spec, fetcher)
+        # Construct a path where the stage should build..
+        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)
+        return stage
+
+    def _make_stage(self):
+        # Construct a composite stage on top of the composite FetchStrategy
+        composite_fetcher = self.fetcher
+        composite_stage = StageComposite()
+        resources = self._get_needed_resources()
+        for ii, fetcher in enumerate(composite_fetcher):
+            if ii == 0:
+                # Construct root stage first
+                stage = self._make_root_stage(fetcher)
+            else:
+                # Construct resource stage
+                resource = resources[ii - 1]  # ii == 0 is root!
+                stage = self._make_resource_stage(composite_stage[0], fetcher, resource)
+            # Append the item to the composite
+            composite_stage.append(stage)
+
+        # Create stage on first access.  Needed because fetch, stage,
+        # patch, and install can be called independently of each
+        # other, so `with self.stage:` in do_install isn't sufficient.
+        composite_stage.create()
+        return composite_stage
 
     @property
     def stage(self):
         if not self.spec.concrete:
             raise ValueError("Can only get a stage for a concrete package.")
-
         if self._stage is None:
-            # Construct a mirror path (TODO: get this out of package.py)
-            mp = spack.mirror.mirror_archive_path(self.spec)
-
-            # Construct a path where the stage should build..
-            s = self.spec
-            stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash())
-
-            # Build the stage
-            self._stage = Stage(self.fetcher, mirror_path=mp, name=stage_name)
-
+            self._stage = self._make_stage()
         return self._stage
 
 
@@ -459,17 +489,27 @@ class Package(object):
         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
+        # associated with the package, append their fetcher to the
+        # composite.
+        root_fetcher = fs.for_package_version(self, self.version)
+        fetcher = fs.FetchStrategyComposite()  # Composite fetcher
+        fetcher.append(root_fetcher)  # Root fetcher is always present
+        resources = self._get_needed_resources()
+        for resource in resources:
+            fetcher.append(resource.fetcher)
+        return fetcher
+
     @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 = fs.for_package_version(self, self.version)
+            self._fetcher = self._make_fetcher()
         return self._fetcher
 
-
     @fetcher.setter
     def fetcher(self, f):
         self._fetcher = f
@@ -631,8 +671,8 @@ class Package(object):
         spack.install_layout.remove_install_directory(self.spec)
 
 
-    def do_fetch(self):
-        """Creates a stage directory and downloads the taball for this package.
+    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.
         """
         if not self.spec.concrete:
@@ -654,79 +694,24 @@ class Package(object):
 
             if not ignore_checksum:
                 raise FetchError(
-                    "Will not fetch %s." % self.spec.format('$_$@'), checksum_msg)
-
-        self.stage.fetch()
+                    "Will not fetch %s" % self.spec.format('$_$@'), checksum_msg)
 
-        ##########
-        # Fetch resources
-        resources = self._get_resources()
-        for resource in resources:
-            resource_stage_folder = self._resource_stage(resource)
-            # FIXME : works only for URLFetchStrategy
-            resource_mirror = join_path(self.name, os.path.basename(resource.fetcher.url))
-            resource_stage = Stage(resource.fetcher, name=resource_stage_folder, mirror_path=resource_mirror)
-            resource.fetcher.set_stage(resource_stage)
-            # Delegate to stage object to trigger mirror logic
-            resource_stage.fetch()
-            resource_stage.check()
-        ##########
+        self.stage.fetch(mirror_only)
 
         self._fetch_time = time.time() - start_time
 
         if spack.do_checksum and self.version in self.versions:
             self.stage.check()
 
-    def do_stage(self):
+
+    def do_stage(self, mirror_only=False):
         """Unpacks the fetched tarball, then changes into the expanded tarball
            directory."""
         if not self.spec.concrete:
             raise ValueError("Can only stage concrete packages.")
 
-        def _expand_archive(stage, name=self.name):
-            archive_dir = stage.source_path
-            if not archive_dir:
-                stage.expand_archive()
-                tty.msg("Created stage in %s." % stage.path)
-            else:
-                tty.msg("Already staged %s in %s." % (name, stage.path))
-
-
-        self.do_fetch()
-        _expand_archive(self.stage)
-
-        ##########
-        # Stage resources in appropriate path
-        resources = self._get_resources()
-        # TODO: this is to allow nested resources, a better solution would be
-        # good
-        for resource in sorted(resources, key=lambda res: len(res.destination)):
-            stage = resource.fetcher.stage
-            _expand_archive(stage, resource.name)
-            # Turn placement into a dict with relative paths
-            placement = os.path.basename(stage.source_path) if resource.placement is None else resource.placement
-            if not isinstance(placement, dict):
-                placement = {'': placement}
-            # Make the paths in the dictionary absolute and link
-            for key, value in placement.iteritems():
-                target_path = join_path(self.stage.source_path, resource.destination)
-                link_path = join_path(target_path, value)
-                source_path = join_path(stage.source_path, key)
-
-                try:
-                    os.makedirs(target_path)
-                except OSError as err:
-                    if err.errno == errno.EEXIST and os.path.isdir(target_path):
-                        pass
-                    else: raise
-
-                # NOTE: a reasonable fix for the TODO above might be to have
-                # these expand in place, but expand_archive does not offer
-                # this
-
-                if not os.path.exists(link_path):
-                    shutil.move(source_path, link_path)
-        ##########
+        self.do_fetch(mirror_only)
+        self.stage.expand_archive()
         self.stage.chdir_to_source()
 
 
@@ -744,7 +729,7 @@ class Package(object):
 
         # If there are no patches, note it.
         if not self.patches and not has_patch_fun:
-            tty.msg("No patches needed for %s." % self.name)
+            tty.msg("No patches needed for %s" % self.name)
             return
 
         # Construct paths to special files in the archive dir used to
@@ -757,7 +742,7 @@ class Package(object):
         # If we encounter an archive that failed to patch, restage it
         # so that we can apply all the patches again.
         if os.path.isfile(bad_file):
-            tty.msg("Patching failed last time.  Restaging.")
+            tty.msg("Patching failed last time. Restaging.")
             self.stage.restage()
 
         self.stage.chdir_to_source()
@@ -767,7 +752,7 @@ class Package(object):
             tty.msg("Already patched %s" % self.name)
             return
         elif os.path.isfile(no_patches_file):
-            tty.msg("No patches needed for %s." % self.name)
+            tty.msg("No patches needed for %s" % self.name)
             return
 
         # Apply all the patches for specs that match this one
@@ -788,10 +773,10 @@ class Package(object):
         if has_patch_fun:
             try:
                 self.patch()
-                tty.msg("Ran patch() for %s." % self.name)
+                tty.msg("Ran patch() for %s" % self.name)
                 patched = True
             except:
-                tty.msg("patch() function failed for %s." % self.name)
+                tty.msg("patch() function failed for %s" % self.name)
                 touch(bad_file)
                 raise
 
@@ -822,12 +807,15 @@ class Package(object):
         mkdirp(self.prefix.man1)
 
 
-    def _get_resources(self):
+    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
+        resources = sorted(resources, key=lambda res: len(res.destination))
         return resources
 
     def _resource_stage(self, resource):
@@ -835,13 +823,9 @@ class Package(object):
         resource_stage_folder = '-'.join(pieces)
         return resource_stage_folder
 
-    def _build_logger(self, log_path):
-        """Create a context manager to log build output."""
-
-
 
     def do_install(self,
-                   keep_prefix=False,  keep_stage=False, ignore_deps=False,
+                   keep_prefix=False,  keep_stage=None, ignore_deps=False,
                    skip_patch=False, verbose=False, make_jobs=None, fake=False):
         """Called by commands to install a package and its dependencies.
 
@@ -850,7 +834,8 @@ class Package(object):
 
         Args:
         keep_prefix -- Keep install prefix on failure. By default, destroys it.
-        keep_stage  -- Keep stage on successful build. By default, destroys it.
+        keep_stage  -- Set to True or false to always keep or always delete stage.
+                       By default, stage is destroyed only if there are no exceptions.
         ignore_deps -- Do not 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.
@@ -860,103 +845,103 @@ class Package(object):
         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
 
-        if os.path.exists(self.prefix):
-            tty.msg("%s is already installed in %s." % (self.name, self.prefix))
+        # 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))
             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)
-
-        start_time = time.time()
-        if not fake:
-            if not skip_patch:
-                self.do_patch()
-            else:
-                self.do_stage()
-
-        # create the install directory.  The install layout
-        # handles this in case so that it can use whatever
-        # package naming scheme it likes.
-        spack.install_layout.create_install_directory(self.spec)
+                fake=fake, skip_patch=skip_patch, verbose=verbose, make_jobs=make_jobs)
 
-        def cleanup():
-            if not keep_prefix:
-                # If anything goes wrong, remove the install prefix
-                self.remove_prefix()
-            else:
-                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)
+        # Set parallelism before starting build.
+        self.make_jobs = make_jobs
 
+        # Then install the package itself.
+        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:
+                    self.do_patch()
+                else:
+                    self.do_stage()
 
-        def real_work():
-            try:
-                tty.msg("Building %s." % self.name)
+            tty.msg("Building %s" % self.name)
 
+            self.stage.keep = keep_stage
+            with self.stage:
                 # Run the pre-install hook in the child process after
                 # the directory is created.
                 spack.hooks.pre_install(self)
 
-                # Set up process's build environment before running install.
                 if fake:
                     self.do_fake_install()
                 else:
                     # Do the real install in the source directory.
-                    self.stage.chdir_to_source()
-
-                    # This redirects 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):
-                        self.install(self.spec, self.prefix)
+                     self.stage.chdir_to_source()
 
-                # Ensure that something was actually installed.
-                self._sanity_check_install()
+                     # Save the build environment in a file before building.
+                     env_path = join_path(os.getcwd(), 'spack-build.env')
 
-                # Move build log into install directory on success
-                if not fake:
-                    log_install_path = spack.install_layout.build_log_path(self.spec)
-                    install(log_path, log_install_path)
+                     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):
+                            dump_environment(env_path)
+                            self.install(self.spec, self.prefix)
 
-                # On successful install, remove the stage.
-                if not keep_stage:
-                    self.stage.destroy()
+                     except ProcessError as e:
+                         # Annotate ProcessErrors with the location of the build log.
+                         e.build_log = log_path
+                         raise e
 
-                # Stop timer.
-                self._total_time = time.time() - start_time
-                build_time = self._total_time - self._fetch_time
+                     # Ensure that something was actually installed.
+                     self._sanity_check_install()
 
-                tty.msg("Successfully installed %s." % self.name,
-                        "Fetch: %s.  Build: %s.  Total: %s."
-                        % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
-                print_pkg(self.prefix)
+                     # 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)
 
-            except ProcessError, e:
-                # Annotate with location of build log.
-                e.build_log = log_path
-                cleanup()
-                raise e
+                     install(log_path, log_install_path)
+                     install(env_path, env_install_path)
+                     dump_packages(self.spec, packages_dir)
 
-            except:
-                # other exceptions just clean up and raise.
-                cleanup()
-                raise
+            # Stop timer.
+            self._total_time = time.time() - start_time
+            build_time = self._total_time - self._fetch_time
 
-        # Set parallelism before starting build.
-        self.make_jobs = make_jobs
+            tty.msg("Successfully installed %s" % self.name,
+                    "Fetch: %s.  Build: %s.  Total: %s."
+                    % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
+            print_pkg(self.prefix)
 
-        # Do the build.
-        spack.build_environment.fork(self, real_work)
+        try:
+            # Create the install prefix and fork the build process.
+            spack.install_layout.create_install_directory(self.spec)
+            spack.build_environment.fork(self, build_process)
+        except:
+            # remove the install prefix if anything went wrong during install.
+            if not keep_prefix:
+                self.remove_prefix()
+            else:
+                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)
+            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.
@@ -1043,7 +1028,7 @@ class Package(object):
         # Uninstalling in Spack only requires removing the prefix.
         self.remove_prefix()
         spack.installed_db.remove(self.spec)
-        tty.msg("Successfully uninstalled %s." % self.spec.short_spec)
+        tty.msg("Successfully uninstalled %s" % self.spec.short_spec)
 
         # Once everything else is done, run post install hooks
         spack.hooks.post_uninstall(self)
@@ -1090,7 +1075,7 @@ 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."
+        tty.msg("Activated extension %s for %s"
                 % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
 
@@ -1142,7 +1127,7 @@ class Package(object):
         if self.activated:
             spack.install_layout.remove_extension(self.extendee_spec, self.spec)
 
-        tty.msg("Deactivated extension %s for %s."
+        tty.msg("Deactivated extension %s for %s"
                 % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
 
@@ -1170,8 +1155,7 @@ class Package(object):
 
     def do_clean(self):
         """Removes the package's build stage and source tarball."""
-        if os.path.exists(self.stage.path):
-            self.stage.destroy()
+        self.stage.destroy()
 
 
     def format_doc(self, **kwargs):
@@ -1210,7 +1194,7 @@ 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)
-        except spack.error.NoNetworkConnectionError, e:
+        except spack.error.NoNetworkConnectionError as e:
             tty.die("Package.fetch_versions couldn't connect to:",
                     e.url, e.message)
 
@@ -1228,8 +1212,8 @@ class Package(object):
 
     @property
     def rpath_args(self):
-        """Get the rpath args as a string, with -Wl,-rpath= for each element."""
-        return " ".join("-Wl,-rpath=%s" % p for p in self.rpath)
+        """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 validate_package_url(url_string):
@@ -1242,6 +1226,52 @@ def validate_package_url(url_string):
         tty.die("Invalid file type in URL: '%s'" % url_string)
 
 
+def dump_packages(spec, path):
+    """Dump all package information for a spec and its dependencies.
+
+       This creates a package repository within path for every
+       namespace in the spec DAG, and fills the repos wtih package
+       files and patch files for every node in the DAG.
+    """
+    mkdirp(path)
+
+    # Copy in package.py files from any dependencies.
+    # Note that we copy them in as they are in the *install* directory
+    # NOT as they are in the repository, because we want a snapshot of
+    # how *this* particular build was done.
+    for node in spec.traverse():
+        if node is not spec:
+            # Locate the dependency package in the install tree and find
+            # its provenance information.
+            source = spack.install_layout.build_packages_path(node)
+            source_repo_root = join_path(source, node.namespace)
+
+            # There's no provenance installed for the source package.  Skip it.
+            # User can always get something current from the builtin repo.
+            if not os.path.isdir(source_repo_root):
+                continue
+
+            # 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)
+
+        # Create a destination repository
+        dest_repo_root = join_path(path, node.namespace)
+        if not os.path.exists(dest_repo_root):
+            spack.repository.create_repo(dest_repo_root)
+        repo = spack.repository.Repo(dest_repo_root)
+
+        # Get the location of the package in the dest repo.
+        dest_pkg_dir = repo.dirname_for_package_name(node.name)
+        if node is not spec:
+            install_tree(source_pkg_dir, dest_pkg_dir)
+        else:
+            spack.repo.dump_provenance(node, dest_pkg_dir)
+
+
 def print_pkg(message):
     """Outputs a message with a package icon."""
     from llnl.util.tty.color import cwrite
@@ -1292,7 +1322,7 @@ 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,
+            "Cannot determine a URL automatically for version %s" % version,
             "Please provide a url for this version in the package.py file.")
 
 
diff --git a/lib/spack/spack/repository.py b/lib/spack/spack/repository.py
index 31596cee7a..3c3ba08bcc 100644
--- a/lib/spack/spack/repository.py
+++ b/lib/spack/spack/repository.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
@@ -33,7 +33,7 @@ from bisect import bisect_left
 from external import yaml
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path
+from llnl.util.filesystem import *
 
 import spack.error
 import spack.config
@@ -156,7 +156,7 @@ class RepoPath(object):
 
         if repo.namespace in self.by_namespace:
             raise DuplicateRepoError(
-                "Package repos '%s' and '%s' both provide namespace %s."
+                "Package repos '%s' and '%s' both provide namespace %s"
                 % (repo.root, self.by_namespace[repo.namespace].root, repo.namespace))
 
         # Add repo to the pkg indexes
@@ -233,6 +233,11 @@ class RepoPath(object):
         return providers
 
 
+    @_autospec
+    def extensions_for(self, extendee_spec):
+        return [p for p in self.all_packages() if p.extends(extendee_spec)]
+
+
     def find_module(self, fullname, path=None):
         """Implements precedence for overlaid namespaces.
 
@@ -295,8 +300,11 @@ class RepoPath(object):
         for repo in self.repos:
             if spec.name in repo:
                 return repo
-        else:
-            raise UnknownPackageError(spec.name)
+
+        # If the package isn't in any repo, return the one with
+        # highest precedence.  This is for commands like `spack edit`
+        # that can operate on packages that don't exist yet.
+        return self.first_repo()
 
 
     @_autospec
@@ -308,6 +316,16 @@ class RepoPath(object):
         return self.repo_for_pkg(spec).get(spec)
 
 
+    @_autospec
+    def dump_provenance(self, spec, path):
+        """Dump provenance information for a spec to a particular path.
+
+           This dumps the package file and any associated patch files.
+           Raises UnknownPackageError if not found.
+        """
+        return self.repo_for_pkg(spec).dump_provenance(spec, path)
+
+
     def dirname_for_package_name(self, pkg_name):
         return self.repo_for_pkg(pkg_name).dirname_for_package_name(pkg_name)
 
@@ -527,7 +545,7 @@ class Repo(object):
             raise UnknownPackageError(spec.name)
 
         if spec.namespace and spec.namespace != self.namespace:
-            raise UnknownPackageError("Repository %s does not contain package %s."
+            raise UnknownPackageError("Repository %s does not contain package %s"
                                       % (self.namespace, spec.fullname))
 
         key = hash(spec)
@@ -544,6 +562,35 @@ class Repo(object):
         return self._instances[key]
 
 
+    @_autospec
+    def dump_provenance(self, spec, path):
+        """Dump provenance information for a spec to a particular path.
+
+           This dumps the package file and any associated patch files.
+           Raises UnknownPackageError if not found.
+        """
+        # Some preliminary checks.
+        if spec.virtual:
+            raise UnknownPackageError(spec.name)
+
+        if spec.namespace and spec.namespace != self.namespace:
+            raise UnknownPackageError("Repository %s does not contain package %s."
+                                      % (self.namespace, spec.fullname))
+
+        # Install any patch files needed by packages.
+        mkdirp(path)
+        for spec, patches in spec.package.patches.items():
+            for patch in patches:
+                if patch.path:
+                    if os.path.exists(patch.path):
+                        install(patch.path, path)
+                    else:
+                        tty.warn("Patch file did not exist: %s" % patch.path)
+
+        # Install the package.py file itself.
+        install(self.filename_for_package_name(spec), path)
+
+
     def purge(self):
         """Clear entire package instance cache."""
         self._instances.clear()
@@ -697,6 +744,58 @@ class Repo(object):
         return self.exists(pkg_name)
 
 
+def create_repo(root, namespace=None):
+    """Create a new repository in root with the specified namespace.
+
+       If the namespace is not provided, use basename of root.
+       Return the canonicalized path and the namespace of the created repository.
+    """
+    root = canonicalize_path(root)
+    if not namespace:
+        namespace = os.path.basename(root)
+
+    if not re.match(r'\w[\.\w-]*', namespace):
+        raise InvalidNamespaceError("'%s' is not a valid namespace." % namespace)
+
+    existed = False
+    if os.path.exists(root):
+        if os.path.isfile(root):
+            raise BadRepoError('File %s already exists and is not a directory' % root)
+        elif os.path.isdir(root):
+            if not os.access(root, os.R_OK | os.W_OK):
+                raise BadRepoError('Cannot create new repo in %s: cannot access directory.' % root)
+            if os.listdir(root):
+                raise BadRepoError('Cannot create new repo in %s: directory is not empty.' % root)
+        existed = True
+
+    full_path = os.path.realpath(root)
+    parent = os.path.dirname(full_path)
+    if not os.access(parent, os.R_OK | os.W_OK):
+        raise BadRepoError("Cannot create repository in %s: can't access parent!" % root)
+
+    try:
+        config_path = os.path.join(root, repo_config_name)
+        packages_path = os.path.join(root, packages_dir_name)
+
+        mkdirp(packages_path)
+        with open(config_path, 'w') as config:
+            config.write("repo:\n")
+            config.write("  namespace: '%s'\n" % namespace)
+
+    except (IOError, OSError) as e:
+        raise BadRepoError('Failed to create new repository in %s.' % root,
+                           "Caused by %s: %s" % (type(e), e))
+
+        # try to clean up.
+        if existed:
+            shutil.rmtree(config_path, ignore_errors=True)
+            shutil.rmtree(packages_path, ignore_errors=True)
+        else:
+            shutil.rmtree(root, ignore_errors=True)
+
+    return full_path, namespace
+
+
 class RepoError(spack.error.SpackError):
     """Superclass for repository-related errors."""
 
@@ -705,6 +804,10 @@ class NoRepoConfiguredError(RepoError):
     """Raised when there are no repositories configured."""
 
 
+class InvalidNamespaceError(RepoError):
+    """Raised when an invalid namespace is encountered."""
+
+
 class BadRepoError(RepoError):
     """Raised when repo layout is invalid."""
 
@@ -722,7 +825,7 @@ class UnknownPackageError(PackageLoadError):
     def __init__(self, name, repo=None):
         msg = None
         if repo:
-            msg = "Package %s not found in repository %s." % (name, repo)
+            msg = "Package %s not found in repository %s" % (name, repo)
         else:
             msg = "Package %s not found." % name
         super(UnknownPackageError, self).__init__(msg)
diff --git a/lib/spack/spack/resource.py b/lib/spack/spack/resource.py
index 2bf92947fd..ddfaaf4cb0 100644
--- a/lib/spack/spack/resource.py
+++ b/lib/spack/spack/resource.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index dcf2dc1e6e..4703a3aae6 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -23,7 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import re
+import errno
 import shutil
 import tempfile
 import sys
@@ -32,46 +32,64 @@ from urlparse import urljoin
 import llnl.util.tty as tty
 from llnl.util.filesystem import *
 
+import spack.util.pattern as pattern
+
 import spack
 import spack.config
 import spack.fetch_strategy as fs
 import spack.error
 
-
 STAGE_PREFIX = 'spack-stage-'
 
 
 class Stage(object):
-    """A Stage object manaages a directory where some source code is
-       downloaded and built before being installed.  It handles
-       fetching the source code, either as an archive to be expanded
-       or by checking it out of a repository.  A stage's lifecycle
-       looks like this:
-
-       Stage()
-         Constructor creates the stage directory.
-       fetch()
-         Fetch a source archive into the stage.
-       expand_archive()
-         Expand the source archive.
-       <install>
-         Build and install the archive.  This is handled by the Package class.
-       destroy()
-         Remove the stage once the package has been installed.
-
-       If spack.use_tmp_stage is True, spack will attempt to create stages
-       in a tmp directory.  Otherwise, stages are created directly in
-       spack.stage_path.
-
-       There are two kinds of stages: named and unnamed.  Named stages can
-       persist between runs of spack, e.g. if you fetched a tarball but
-       didn't finish building it, you won't have to fetch it again.
-
-       Unnamed stages are created using standard mkdtemp mechanisms or
-       similar, and are intended to persist for only one run of spack.
+    """Manages a temporary stage directory for building.
+
+    A Stage object is a context manager that handles a directory where
+    some source code is downloaded and built before being installed.
+    It handles fetching the source code, either as an archive to be
+    expanded or by checking it out of a repository.  A stage's
+    lifecycle looks like this:
+
+    ```
+    with Stage() as stage:      # Context manager creates and destroys the stage directory
+        stage.fetch()           # Fetch a source archive into the stage.
+        stage.expand_archive()  # Expand the source archive.
+        <install>               # Build and install the archive. (handled by user of Stage)
+    ```
+
+    When used as a context manager, the stage is automatically
+    destroyed if no exception is raised by the context. If an
+    excpetion is raised, the stage is left in the filesystem and NOT
+    destroyed, for potential reuse later.
+
+    You can also use the stage's create/destroy functions manually,
+    like this:
+
+    ```
+    stage = Stage()
+    try:
+        stage.create()          # Explicitly create the stage directory.
+        stage.fetch()           # Fetch a source archive into the stage.
+        stage.expand_archive()  # Expand the source archive.
+        <install>               # Build and install the archive. (handled by user of Stage)
+    finally:
+        stage.destroy()         # Explicitly destroy the stage directory.
+    ```
+
+    If spack.use_tmp_stage is True, spack will attempt to create
+    stages in a tmp directory.  Otherwise, stages are created directly
+    in spack.stage_path.
+
+    There are two kinds of stages: named and unnamed.  Named stages
+    can persist between runs of spack, e.g. if you fetched a tarball
+    but didn't finish building it, you won't have to fetch it again.
+
+    Unnamed stages are created using standard mkdtemp mechanisms or
+    similar, and are intended to persist for only one run of spack.
     """
 
-    def __init__(self, url_or_fetch_strategy, **kwargs):
+    def __init__(self, url_or_fetch_strategy, name=None, mirror_path=None, keep=None):
         """Create a stage object.
            Parameters:
              url_or_fetch_strategy
@@ -83,6 +101,18 @@ class Stage(object):
                  and will persist between runs (or if you construct another
                  stage object later).  If name is not provided, then this
                  stage will be given a unique name automatically.
+
+             mirror_path
+                 If provided, Stage will search Spack's mirrors for
+                 this archive at the mirror_path, before using the
+                 default fetch strategy.
+
+             keep
+                 By default, when used as a context manager, the Stage
+                 is cleaned up when everything goes well, and it is
+                 kept intact when an exception is raised. You can
+                 override this behavior by setting keep to True
+                 (always keep) or False (always delete).
         """
         # TODO: fetch/stage coupling needs to be reworked -- the logic
         # TODO: here is convoluted and not modular enough.
@@ -94,25 +124,56 @@ class Stage(object):
             raise ValueError("Can't construct Stage without url or fetch strategy")
         self.fetcher.set_stage(self)
         self.default_fetcher = self.fetcher  # self.fetcher can change with mirrors.
-        self.skip_checksum_for_mirror = True # used for mirrored archives of repositories.
+        self.skip_checksum_for_mirror = True  # used for mirrored archives of repositories.
+
+        # TODO : this uses a protected member of tempfile, but seemed the only way to get a temporary name
+        # TODO : besides, the temporary link name won't be the same as the temporary stage area in tmp_root
+        self.name = name
+        if name is None:
+            self.name = STAGE_PREFIX + next(tempfile._get_candidate_names())
+        self.mirror_path = mirror_path
+        self.tmp_root = find_tmp_root()
 
-        self.name = kwargs.get('name')
-        self.mirror_path = kwargs.get('mirror_path')
+        # 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)
 
-        self.tmp_root = find_tmp_root()
+        # Flag to decide whether to delete the stage folder on exit or not
+        self.keep = keep
 
-        self.path = None
-        self._setup()
 
+    def __enter__(self):
+        """
+        Entering a stage context will create the stage directory
+
+        Returns:
+            self
+        """
+        self.create()
+        return self
 
-    def _cleanup_dead_links(self):
-        """Remove any dead links in the stage directory."""
-        for file in os.listdir(spack.stage_path):
-            path = join_path(spack.stage_path, file)
-            if os.path.islink(path):
-                real_path = os.path.realpath(path)
-                if not os.path.exists(path):
-                    os.unlink(path)
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        """
+        Exiting from a stage context will delete the stage directory unless:
+        - it was explicitly requested not to do so
+        - an exception has been raised
+
+        Args:
+            exc_type: exception type
+            exc_val: exception value
+            exc_tb: exception traceback
+
+        Returns:
+            Boolean
+        """
+        if self.keep is None:
+            # Default: delete when there are no exceptions.
+            if exc_type is None: self.destroy()
+
+        elif not self.keep:
+            # Overridden. Either always keep or always delete.
+            self.destroy()
 
 
     def _need_to_create_path(self):
@@ -132,7 +193,7 @@ class Stage(object):
         # Path looks ok, but need to check the target of the link.
         if os.path.islink(self.path):
             real_path = os.path.realpath(self.path)
-            real_tmp  = os.path.realpath(self.tmp_root)
+            real_tmp = os.path.realpath(self.tmp_root)
 
             if spack.use_tmp_stage:
                 # If we're using a tmp dir, it's a link, and it points at the right spot,
@@ -151,56 +212,6 @@ class Stage(object):
 
         return False
 
-
-    def _setup(self):
-        """Creates the stage directory.
-           If spack.use_tmp_stage is False, the stage directory is created
-           directly under spack.stage_path.
-
-           If spack.use_tmp_stage is True, this will attempt to create a
-           stage in a temporary directory and link it into spack.stage_path.
-           Spack will use the first writable location in spack.tmp_dirs to
-           create a stage.  If there is no valid location in tmp_dirs, fall
-           back to making the stage inside spack.stage_path.
-        """
-        # Create the top-level stage directory
-        mkdirp(spack.stage_path)
-        self._cleanup_dead_links()
-
-        # If this is a named stage, then construct a named path.
-        if self.name is not None:
-            self.path = join_path(spack.stage_path, self.name)
-
-        # If this is a temporary stage, them make the temp directory
-        tmp_dir = None
-        if self.tmp_root:
-            if self.name is None:
-                # Unnamed tmp root.  Link the path in
-                tmp_dir = tempfile.mkdtemp('', STAGE_PREFIX, self.tmp_root)
-                self.name = os.path.basename(tmp_dir)
-                self.path = join_path(spack.stage_path, self.name)
-                if self._need_to_create_path():
-                    os.symlink(tmp_dir, self.path)
-
-            else:
-                if self._need_to_create_path():
-                    tmp_dir = tempfile.mkdtemp('', STAGE_PREFIX, self.tmp_root)
-                    os.symlink(tmp_dir, self.path)
-
-        # if we're not using a tmp dir, create the stage directly in the
-        # stage dir, rather than linking to it.
-        else:
-            if self.name is None:
-                self.path = tempfile.mkdtemp('', STAGE_PREFIX, spack.stage_path)
-                self.name = os.path.basename(self.path)
-            else:
-                if self._need_to_create_path():
-                    mkdirp(self.path)
-
-        # Make sure we can actually do something with the stage we made.
-        ensure_access(self.path)
-
-
     @property
     def archive_file(self):
         """Path to the source archive within this stage directory."""
@@ -217,35 +228,43 @@ class Stage(object):
         else:
             return None
 
-
     @property
     def source_path(self):
-        """Returns the path to the expanded/checked out source code
-           within this fetch strategy's path.
+        """Returns the path to the expanded/checked out source code.
+
+        To find the source code, this method searches for the first
+        subdirectory of the stage that it can find, and returns it.
+        This assumes nothing besides the archive file will be in the
+        stage path, but it has the advantage that we don't need to
+        know the name of the archive or its contents.
 
-           This assumes nothing else is going ot be put in the
-           FetchStrategy's path.  It searches for the first
-           subdirectory of the path it can find, then returns that.
+        If the fetch strategy is not supposed to expand the downloaded
+        file, it will just return the stage path. If the archive needs
+        to be expanded, it will return None when no archive is found.
         """
+        if isinstance(self.fetcher, fs.URLFetchStrategy):
+            if not self.fetcher.expand_archive:
+                return self.path
+
         for p in [os.path.join(self.path, f) for f in os.listdir(self.path)]:
             if os.path.isdir(p):
                 return p
         return None
 
-
     def chdir(self):
         """Changes directory to the stage path.  Or dies if it is not set up."""
         if os.path.isdir(self.path):
             os.chdir(self.path)
         else:
-            tty.die("Setup failed: no such directory: " + self.path)
-
+            raise ChdirError("Setup failed: no such directory: " + self.path)
 
-    def fetch(self):
+    def fetch(self, mirror_only=False):
         """Downloads an archive or checks out code from a repository."""
         self.chdir()
 
-        fetchers = [self.default_fetcher]
+        fetchers = []
+        if not mirror_only:
+            fetchers.append(self.default_fetcher)
 
         # TODO: move mirror logic out of here and clean it up!
         # TODO: Or @alalazo may have some ideas about how to use a
@@ -253,7 +272,13 @@ class Stage(object):
         self.skip_checksum_for_mirror = True
         if self.mirror_path:
             mirrors = spack.config.get_config('mirrors')
-            urls = [urljoin(u, self.mirror_path) for name, u in mirrors.items()]
+
+            # Join URLs of mirror roots with mirror paths. Because
+            # urljoin() will strip everything past the final '/' in
+            # the root, so we add a '/' if it is not present.
+            mirror_roots = [root if root.endswith('/') else root + '/'
+                            for root in mirrors.values()]
+            urls = [urljoin(root, self.mirror_path) for root in mirror_roots]
 
             # If this archive is normally fetched from a tarball URL,
             # then use the same digest.  `spack mirror` ensures that
@@ -262,10 +287,11 @@ class Stage(object):
             if isinstance(self.default_fetcher, fs.URLFetchStrategy):
                 digest = self.default_fetcher.digest
 
-            # Have to skip the checkesum for things archived from
+            # Have to skip the checksum for things archived from
             # repositories.  How can this be made safer?
             self.skip_checksum_for_mirror = not bool(digest)
 
+            # Add URL strategies for all the mirrors with the digest
             for url in urls:
                 fetchers.insert(0, fs.URLFetchStrategy(url, digest))
 
@@ -275,7 +301,7 @@ class Stage(object):
                 self.fetcher = fetcher
                 self.fetcher.fetch()
                 break
-            except spack.error.SpackError, e:
+            except spack.error.SpackError as e:
                 tty.msg("Fetching from %s failed." % fetcher)
                 tty.debug(e)
                 continue
@@ -284,7 +310,6 @@ class Stage(object):
             self.fetcher = self.default_fetcher
             raise fs.FetchError(errMessage, None)
 
-
     def check(self):
         """Check the downloaded archive against a checksum digest.
            No-op if this stage checks code out of a repository."""
@@ -298,14 +323,17 @@ class Stage(object):
         else:
             self.fetcher.check()
 
-
     def expand_archive(self):
         """Changes to the stage directory and attempt to expand the downloaded
            archive.  Fail if the stage is not set up or if the archive is not yet
            downloaded.
         """
-        self.fetcher.expand()
-
+        archive_dir = self.source_path
+        if not archive_dir:
+            self.fetcher.expand()
+            tty.msg("Created stage in %s" % self.path)
+        else:
+            tty.msg("Already staged %s in %s" % (self.name, self.path))
 
     def chdir_to_source(self):
         """Changes directory to the expanded archive directory.
@@ -319,16 +347,41 @@ class Stage(object):
             if not os.listdir(path):
                 tty.die("Archive was empty for %s" % self.name)
 
-
     def restage(self):
         """Removes the expanded archive path if it exists, then re-expands
            the archive.
         """
         self.fetcher.reset()
 
+    def create(self):
+        """
+        Creates the stage directory
+
+        If self.tmp_root evaluates to False, the stage directory is
+        created directly under spack.stage_path, otherwise this will
+        attempt to create a stage in a temporary directory and link it
+        into spack.stage_path.
+
+        Spack will use the first writable location in spack.tmp_dirs
+        to create a stage. If there is no valid location in tmp_dirs,
+        fall back to making the stage inside spack.stage_path.
+        """
+        # Create the top-level stage directory
+        mkdirp(spack.stage_path)
+        remove_dead_links(spack.stage_path)
+        # If a tmp_root exists then create a directory there and then link it in the stage area,
+        # otherwise create the stage directory in self.path
+        if self._need_to_create_path():
+            if self.tmp_root:
+                tmp_dir = tempfile.mkdtemp('', STAGE_PREFIX, self.tmp_root)
+                os.symlink(tmp_dir, self.path)
+            else:
+                mkdirp(self.path)
+        # Make sure we can actually do something with the stage we made.
+        ensure_access(self.path)
 
     def destroy(self):
-        """Remove this stage directory."""
+        """Removes this stage directory."""
         remove_linked_tree(self.path)
 
         # Make sure we don't end up in a removed directory
@@ -338,8 +391,82 @@ class Stage(object):
             os.chdir(os.path.dirname(self.path))
 
 
+class ResourceStage(Stage):
+    def __init__(self, url_or_fetch_strategy, root, resource, **kwargs):
+        super(ResourceStage, self).__init__(url_or_fetch_strategy, **kwargs)
+        self.root_stage = root
+        self.resource = resource
+
+    def expand_archive(self):
+        super(ResourceStage, self).expand_archive()
+        root_stage = self.root_stage
+        resource = self.resource
+        placement = os.path.basename(self.source_path) if resource.placement is None else resource.placement
+        if not isinstance(placement, dict):
+            placement = {'': placement}
+        # Make the paths in the dictionary absolute and link
+        for key, value in placement.iteritems():
+            target_path = join_path(root_stage.source_path, resource.destination)
+            destination_path = join_path(target_path, value)
+            source_path = join_path(self.source_path, key)
+
+            try:
+                os.makedirs(target_path)
+            except OSError as err:
+                if err.errno == errno.EEXIST and os.path.isdir(target_path):
+                    pass
+                else:
+                    raise
+
+            if not os.path.exists(destination_path):
+                # Create a symlink
+                tty.info('Moving resource stage\n\tsource : {stage}\n\tdestination : {destination}'.format(
+                    stage=source_path, destination=destination_path
+                ))
+                shutil.move(source_path, destination_path)
+
+
+@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive',  'restage', 'destroy'])
+class StageComposite:
+    """
+    Composite for Stage type objects. The first item in this composite is considered to be the root package, and
+    operations that return a value are forwarded to it.
+    """
+    #
+    # __enter__ and __exit__ delegate to all stages in the composite.
+    #
+    def __enter__(self):
+        for item in self:
+            item.__enter__()
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        for item in reversed(self):
+            item.keep = getattr(self, 'keep', None)
+            item.__exit__(exc_type, exc_val, exc_tb)
+
+    #
+    # Below functions act only on the *first* stage in the composite.
+    #
+    @property
+    def source_path(self):
+        return self[0].source_path
+
+    @property
+    def path(self):
+        return self[0].path
+
+    def chdir_to_source(self):
+        return self[0].chdir_to_source()
+
+    @property
+    def archive_file(self):
+        return self[0].archive_file
+
+
 class DIYStage(object):
     """Simple class that allows any directory to be a spack stage."""
+
     def __init__(self, path):
         self.archive_file = None
         self.path = path
@@ -349,12 +476,16 @@ class DIYStage(object):
         if os.path.isdir(self.path):
             os.chdir(self.path)
         else:
-            tty.die("Setup failed: no such directory: " + self.path)
+            raise ChdirError("Setup failed: no such directory: " + self.path)
+
+    # DIY stages do nothing as context managers.
+    def __enter__(self): pass
+    def __exit__(self, exc_type, exc_val, exc_tb): pass
 
     def chdir_to_source(self):
         self.chdir()
 
-    def fetch(self):
+    def fetch(self, mirror_only):
         tty.msg("No need to fetch for DIY.")
 
     def check(self):
@@ -383,19 +514,6 @@ def ensure_access(file=spack.stage_path):
         tty.die("Insufficient permissions for %s" % file)
 
 
-def remove_linked_tree(path):
-    """Removes a directory and its contents.  If the directory is a symlink,
-       follows the link and reamoves the real directory before removing the
-       link.
-    """
-    if os.path.exists(path):
-        if os.path.islink(path):
-            shutil.rmtree(os.path.realpath(path), True)
-            os.unlink(path)
-        else:
-            shutil.rmtree(path, True)
-
-
 def purge():
     """Remove all build directories in the top-level stage path."""
     if os.path.isdir(spack.stage_path):
@@ -424,19 +542,15 @@ def find_tmp_root():
 
 
 class StageError(spack.error.SpackError):
-    def __init__(self, message, long_message=None):
-        super(self, StageError).__init__(message, long_message)
+    """"Superclass for all errors encountered during staging."""
 
 
 class RestageError(StageError):
-    def __init__(self, message, long_msg=None):
-        super(RestageError, self).__init__(message, long_msg)
+    """"Error encountered during restaging."""
 
 
 class ChdirError(StageError):
-    def __init__(self, message, long_msg=None):
-        super(ChdirError, self).__init__(message, long_msg)
-
+    """Raised when Spack can't change directories."""
 
 # Keep this in namespace for convenience
 FailedDownloadError = fs.FailedDownloadError
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index a569cbbf35..4b9a361d4b 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -48,6 +48,7 @@ test_names = ['versions',
               'package_sanity',
               'config',
               'directory_layout',
+              'pattern',
               'python_version',
               'git_fetch',
               'svn_fetch',
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index 905af28a06..f3f6d4a22e 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -39,11 +39,11 @@ test_command = [
     'arg1',
     '-Wl,--start-group',
     'arg2',
-    '-Wl,-rpath=/first/rpath', 'arg3', '-Wl,-rpath', '-Wl,/second/rpath',
+    '-Wl,-rpath,/first/rpath', 'arg3', '-Wl,-rpath', '-Wl,/second/rpath',
     '-llib1', '-llib2',
     'arg4',
     '-Wl,--end-group',
-    '-Xlinker,-rpath', '-Xlinker,/third/rpath', '-Xlinker,-rpath=/fourth/rpath',
+    '-Xlinker', '-rpath', '-Xlinker', '/third/rpath', '-Xlinker', '-rpath', '-Xlinker', '/fourth/rpath',
     '-llib3', '-llib4',
     'arg5', 'arg6']
 
@@ -95,13 +95,13 @@ class CompilerTest(unittest.TestCase):
     def test_ccld_mode(self):
         self.check_cc('dump-mode', [], "ccld")
         self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld")
-        self.check_cc('dump-mode', ['foo.c', '-o', 'foo', '-Wl,-rpath=foo'], "ccld")
-        self.check_cc('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath=foo'], "ccld")
+        self.check_cc('dump-mode', ['foo.c', '-o', 'foo', '-Wl,-rpath,foo'], "ccld")
+        self.check_cc('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ccld")
 
 
     def test_ld_mode(self):
         self.check_ld('dump-mode', [], "ld")
-        self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath=foo'], "ld")
+        self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld")
 
 
     def test_includes(self):
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 3cdbfa7de9..820c5d84a8 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -22,8 +22,6 @@
 # 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 spack
 from spack.spec import Spec, CompilerSpec
 from spack.test.mock_packages_test import *
diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py
index d8be5a855b..0562d2d620 100644
--- a/lib/spack/spack/test/config.py
+++ b/lib/spack/spack/test/config.py
@@ -22,13 +22,13 @@
 # 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 shutil
 import os
+import shutil
 from tempfile import mkdtemp
-from ordereddict_backport import OrderedDict
+
 import spack
 import spack.config
+from ordereddict_backport import OrderedDict
 from spack.test.mock_packages_test import *
 
 # Some sample compiler config data
diff --git a/lib/spack/spack/test/configure_guess.py b/lib/spack/spack/test/configure_guess.py
index a4e8565b62..2440d120e5 100644
--- a/lib/spack/spack/test/configure_guess.py
+++ b/lib/spack/spack/test/configure_guess.py
@@ -23,20 +23,15 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import unittest
 import shutil
 import tempfile
+import unittest
 
 from llnl.util.filesystem import *
-
 from spack.cmd.create import ConfigureGuesser
 from spack.stage import Stage
-
-from spack.fetch_strategy import URLFetchStrategy
-from spack.directory_layout import YamlDirectoryLayout
-from spack.util.executable import which
 from spack.test.mock_packages_test import *
-from spack.test.mock_repo import MockArchive
+from spack.util.executable import which
 
 
 class InstallTest(unittest.TestCase):
@@ -52,8 +47,6 @@ class InstallTest(unittest.TestCase):
 
     def tearDown(self):
         shutil.rmtree(self.tmpdir, ignore_errors=True)
-        if self.stage:
-            self.stage.destroy()
         os.chdir(self.orig_dir)
 
 
@@ -64,12 +57,12 @@ class InstallTest(unittest.TestCase):
 
         url = 'file://' + join_path(os.getcwd(), 'archive.tar.gz')
         print url
-        self.stage = Stage(url)
-        self.stage.fetch()
+        with Stage(url) as stage:
+            stage.fetch()
 
-        guesser = ConfigureGuesser()
-        guesser(self.stage)
-        self.assertEqual(system, guesser.build_system)
+            guesser = ConfigureGuesser()
+            guesser(stage)
+            self.assertEqual(system, guesser.build_system)
 
 
     def test_python(self):
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index 0205f4b8ce..9a57e1f03e 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -26,19 +26,18 @@
 These tests check the database is functioning properly,
 both in memory and in its file
 """
-import tempfile
-import shutil
 import multiprocessing
-
-from llnl.util.lock import *
-from llnl.util.filesystem import join_path
+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 llnl.util.tty.colify import colify
 
 def _print_ref_counts():
     """Print out all ref counts for the graph used here, for debugging"""
diff --git a/lib/spack/spack/test/directory_layout.py b/lib/spack/spack/test/directory_layout.py
index 8412f4a9b4..8ad8f1a360 100644
--- a/lib/spack/spack/test/directory_layout.py
+++ b/lib/spack/spack/test/directory_layout.py
@@ -25,20 +25,17 @@
 """\
 This test verifies that the Spack directory layout works properly.
 """
-import unittest
-import tempfile
-import shutil
 import os
-
-from llnl.util.filesystem import *
+import shutil
+import tempfile
 
 import spack
-from spack.spec import Spec
-from spack.repository import RepoPath
+from llnl.util.filesystem import *
 from spack.directory_layout import YamlDirectoryLayout
+from spack.repository import RepoPath
+from spack.spec import Spec
 from spack.test.mock_packages_test import *
 
-
 # number of packages to test (to reduce test time)
 max_packages = 10
 
diff --git a/lib/spack/spack/test/git_fetch.py b/lib/spack/spack/test/git_fetch.py
index 3813079065..3578044116 100644
--- a/lib/spack/spack/test/git_fetch.py
+++ b/lib/spack/spack/test/git_fetch.py
@@ -23,19 +23,12 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import unittest
-import shutil
-import tempfile
-
-from llnl.util.filesystem import *
 
 import spack
-from spack.version import ver
-from spack.stage import Stage
-from spack.util.executable import which
-
+from llnl.util.filesystem import *
 from spack.test.mock_packages_test import *
 from spack.test.mock_repo import MockGitRepo
+from spack.version import ver
 
 
 class GitFetchTest(MockPackagesTest):
@@ -52,22 +45,15 @@ class GitFetchTest(MockPackagesTest):
         spec.concretize()
         self.pkg = spack.repo.get(spec, new=True)
 
-
     def tearDown(self):
         """Destroy the stage space used by this test."""
         super(GitFetchTest, self).tearDown()
-
-        if self.repo.stage is not None:
-            self.repo.stage.destroy()
-
-        self.pkg.do_clean()
-
+        self.repo.destroy()
 
     def assert_rev(self, rev):
         """Check that the current git revision is equal to the supplied rev."""
         self.assertEqual(self.repo.rev_hash('HEAD'), self.repo.rev_hash(rev))
 
-
     def try_fetch(self, rev, test_file, args):
         """Tries to:
            1. Fetch the repo using a fetch strategy constructed with
@@ -79,26 +65,27 @@ class GitFetchTest(MockPackagesTest):
         """
         self.pkg.versions[ver('git')] = args
 
-        self.pkg.do_stage()
-        self.assert_rev(rev)
+        with self.pkg.stage:
+            self.pkg.do_stage()
+            self.assert_rev(rev)
 
-        file_path = join_path(self.pkg.stage.source_path, test_file)
-        self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
-        self.assertTrue(os.path.isfile(file_path))
+            file_path = join_path(self.pkg.stage.source_path, test_file)
+            self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
+            self.assertTrue(os.path.isfile(file_path))
 
-        os.unlink(file_path)
-        self.assertFalse(os.path.isfile(file_path))
+            os.unlink(file_path)
+            self.assertFalse(os.path.isfile(file_path))
 
-        untracked_file = 'foobarbaz'
-        touch(untracked_file)
-        self.assertTrue(os.path.isfile(untracked_file))
-        self.pkg.do_restage()
-        self.assertFalse(os.path.isfile(untracked_file))
+            untracked_file = 'foobarbaz'
+            touch(untracked_file)
+            self.assertTrue(os.path.isfile(untracked_file))
+            self.pkg.do_restage()
+            self.assertFalse(os.path.isfile(untracked_file))
 
-        self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
-        self.assertTrue(os.path.isfile(file_path))
+            self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
+            self.assertTrue(os.path.isfile(file_path))
 
-        self.assert_rev(rev)
+            self.assert_rev(rev)
 
 
     def test_fetch_master(self):
diff --git a/lib/spack/spack/test/hg_fetch.py b/lib/spack/spack/test/hg_fetch.py
index ee8327aec8..b8a0c1ec46 100644
--- a/lib/spack/spack/test/hg_fetch.py
+++ b/lib/spack/spack/test/hg_fetch.py
@@ -23,16 +23,12 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import unittest
-
-from llnl.util.filesystem import *
-
 import spack
+
 from spack.version import ver
-from spack.stage import Stage
-from spack.util.executable import which
-from spack.test.mock_packages_test import *
 from spack.test.mock_repo import MockHgRepo
+from llnl.util.filesystem import *
+from spack.test.mock_packages_test import *
 
 
 class HgFetchTest(MockPackagesTest):
@@ -49,16 +45,10 @@ class HgFetchTest(MockPackagesTest):
         spec.concretize()
         self.pkg = spack.repo.get(spec, new=True)
 
-
     def tearDown(self):
         """Destroy the stage space used by this test."""
         super(HgFetchTest, self).tearDown()
-
-        if self.repo.stage is not None:
-            self.repo.stage.destroy()
-
-        self.pkg.do_clean()
-
+        self.repo.destroy()
 
     def try_fetch(self, rev, test_file, args):
         """Tries to:
@@ -71,26 +61,27 @@ class HgFetchTest(MockPackagesTest):
         """
         self.pkg.versions[ver('hg')] = args
 
-        self.pkg.do_stage()
-        self.assertEqual(self.repo.get_rev(), rev)
+        with self.pkg.stage:
+            self.pkg.do_stage()
+            self.assertEqual(self.repo.get_rev(), rev)
 
-        file_path = join_path(self.pkg.stage.source_path, test_file)
-        self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
-        self.assertTrue(os.path.isfile(file_path))
+            file_path = join_path(self.pkg.stage.source_path, test_file)
+            self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
+            self.assertTrue(os.path.isfile(file_path))
 
-        os.unlink(file_path)
-        self.assertFalse(os.path.isfile(file_path))
+            os.unlink(file_path)
+            self.assertFalse(os.path.isfile(file_path))
 
-        untracked = 'foobarbaz'
-        touch(untracked)
-        self.assertTrue(os.path.isfile(untracked))
-        self.pkg.do_restage()
-        self.assertFalse(os.path.isfile(untracked))
+            untracked = 'foobarbaz'
+            touch(untracked)
+            self.assertTrue(os.path.isfile(untracked))
+            self.pkg.do_restage()
+            self.assertFalse(os.path.isfile(untracked))
 
-        self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
-        self.assertTrue(os.path.isfile(file_path))
+            self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
+            self.assertTrue(os.path.isfile(file_path))
 
-        self.assertEqual(self.repo.get_rev(), rev)
+            self.assertEqual(self.repo.get_rev(), rev)
 
 
     def test_fetch_default(self):
diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py
index 628329a423..8297893f01 100644
--- a/lib/spack/spack/test/install.py
+++ b/lib/spack/spack/test/install.py
@@ -22,18 +22,13 @@
 # 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
 import shutil
 import tempfile
 
-from llnl.util.filesystem import *
-
 import spack
-from spack.stage import Stage
-from spack.fetch_strategy import URLFetchStrategy
+from llnl.util.filesystem import *
 from spack.directory_layout import YamlDirectoryLayout
-from spack.util.executable import which
+from spack.fetch_strategy import URLFetchStrategy, FetchStrategyComposite
 from spack.test.mock_packages_test import *
 from spack.test.mock_repo import MockArchive
 
@@ -59,9 +54,7 @@ class InstallTest(MockPackagesTest):
 
     def tearDown(self):
         super(InstallTest, self).tearDown()
-
-        if self.repo.stage is not None:
-            self.repo.stage.destroy()
+        self.repo.destroy()
 
         # Turn checksumming back on
         spack.do_checksum = True
@@ -81,7 +74,10 @@ class InstallTest(MockPackagesTest):
         pkg = spack.repo.get(spec)
 
         # Fake the URL for the package so it downloads from a file.
-        pkg.fetcher = URLFetchStrategy(self.repo.url)
+
+        fetcher = FetchStrategyComposite()
+        fetcher.append(URLFetchStrategy(self.repo.url))
+        pkg.fetcher = fetcher
 
         try:
             pkg.do_install()
diff --git a/lib/spack/spack/test/link_tree.py b/lib/spack/spack/test/link_tree.py
index 886b7ef4c5..ee37e765c7 100644
--- a/lib/spack/spack/test/link_tree.py
+++ b/lib/spack/spack/test/link_tree.py
@@ -24,8 +24,6 @@
 ##############################################################################
 import os
 import unittest
-import shutil
-import tempfile
 
 from llnl.util.filesystem import *
 from llnl.util.link_tree import LinkTree
@@ -38,6 +36,7 @@ class LinkTreeTest(unittest.TestCase):
 
     def setUp(self):
         self.stage = Stage('link-tree-test')
+        self.stage.create()
 
         with working_dir(self.stage.path):
             touchp('source/1')
@@ -51,10 +50,8 @@ class LinkTreeTest(unittest.TestCase):
         source_path = os.path.join(self.stage.path, 'source')
         self.link_tree = LinkTree(source_path)
 
-
     def tearDown(self):
-        if self.stage:
-            self.stage.destroy()
+        self.stage.destroy()
 
 
     def check_file_link(self, filename):
diff --git a/lib/spack/spack/test/lock.py b/lib/spack/spack/test/lock.py
index bc68df01db..3b11d18da4 100644
--- a/lib/spack/spack/test/lock.py
+++ b/lib/spack/spack/test/lock.py
@@ -25,15 +25,13 @@
 """
 These tests ensure that our lock works correctly.
 """
-import unittest
-import os
-import tempfile
 import shutil
+import tempfile
+import unittest
 from multiprocessing import Process
 
-from llnl.util.lock import *
 from llnl.util.filesystem import join_path, touch
-
+from llnl.util.lock import *
 from spack.util.multiproc import Barrier
 
 # This is the longest a failed test will take, as the barriers will
diff --git a/lib/spack/spack/test/make_executable.py b/lib/spack/spack/test/make_executable.py
index d568a28d44..a2606acf19 100644
--- a/lib/spack/spack/test/make_executable.py
+++ b/lib/spack/spack/test/make_executable.py
@@ -28,13 +28,13 @@ Tests for Spack's built-in parallel make support.
 This just tests whether the right args are getting passed to make.
 """
 import os
-import unittest
-import tempfile
 import shutil
+import tempfile
+import unittest
 
 from llnl.util.filesystem import *
-from spack.util.environment import path_put_first
 from spack.build_environment import MakeExecutable
+from spack.util.environment import path_put_first
 
 
 class MakeExecutableTest(unittest.TestCase):
diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py
index 04e9e3db2e..e707adfe9d 100644
--- a/lib/spack/spack/test/mirror.py
+++ b/lib/spack/spack/test/mirror.py
@@ -23,11 +23,10 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-from filecmp import dircmp
-
 import spack
 import spack.mirror
-from spack.util.compression import decompressor_for
+
+from filecmp import dircmp
 from spack.test.mock_packages_test import *
 from spack.test.mock_repo import *
 
@@ -44,8 +43,16 @@ class MirrorTest(MockPackagesTest):
         self.repos = {}
 
 
+    def tearDown(self):
+        """Destroy all the stages created by the repos in setup."""
+        super(MirrorTest, self).tearDown()
+        for repo in self.repos.values():
+            repo.destroy()
+        self.repos.clear()
+
+
     def set_up_package(self, name, MockRepoClass, url_attr):
-        """Use this to set up a mock package to be mirrored.
+        """Set up a mock package to be mirrored.
            Each package needs us to:
              1. Set up a mock repo/archive to fetch from.
              2. Point the package's version args at that repo.
@@ -65,22 +72,15 @@ class MirrorTest(MockPackagesTest):
         pkg.versions[v][url_attr] = repo.url
 
 
-    def tearDown(self):
-        """Destroy all the stages created by the repos in setup."""
-        super(MirrorTest, self).tearDown()
-
-        for name, repo in self.repos.items():
-            if repo.stage:
-                pass #repo.stage.destroy()
-
-        self.repos.clear()
+    def check_mirror(self):
+        with Stage('spack-mirror-test') as stage:
+            mirror_root = join_path(stage.path, 'test-mirror')
 
+            # register mirror with spack config
+            mirrors = { 'spack-mirror-test' : 'file://' + mirror_root }
+            spack.config.update_config('mirrors', mirrors)
 
-    def check_mirror(self):
-        stage = Stage('spack-mirror-test')
-        mirror_root = join_path(stage.path, 'test-mirror')
 
-        try:
             os.chdir(stage.path)
             spack.mirror.create(
                 mirror_root, self.repos, no_checksum=True)
@@ -88,7 +88,7 @@ class MirrorTest(MockPackagesTest):
             # Stage directory exists
             self.assertTrue(os.path.isdir(mirror_root))
 
-            # subdirs for each package
+            # check that there are subdirs for each package
             for name in self.repos:
                 subdir = join_path(mirror_root, name)
                 self.assertTrue(os.path.isdir(subdir))
@@ -96,40 +96,28 @@ class MirrorTest(MockPackagesTest):
                 files = os.listdir(subdir)
                 self.assertEqual(len(files), 1)
 
-                # Decompress archive in the mirror
-                archive = files[0]
-                archive_path = join_path(subdir, archive)
-                decomp = decompressor_for(archive_path)
-
-                with working_dir(subdir):
-                    decomp(archive_path)
-
-                    # Find the untarred archive directory.
-                    files = os.listdir(subdir)
-                    self.assertEqual(len(files), 2)
-                    self.assertTrue(archive in files)
-                    files.remove(archive)
-
-                    expanded_archive = join_path(subdir, files[0])
-                    self.assertTrue(os.path.isdir(expanded_archive))
-
-                    # Compare the original repo with the expanded archive
-                    repo = self.repos[name]
-                    if not 'svn' in name:
-                        original_path = repo.path
-                    else:
-                        co = 'checked_out'
-                        svn('checkout', repo.url, co)
-                        original_path = join_path(subdir, co)
-
-                    dcmp = dircmp(original_path, expanded_archive)
-
-                    # make sure there are no new files in the expanded tarball
-                    self.assertFalse(dcmp.right_only)
-                    self.assertTrue(all(l in exclude for l in dcmp.left_only))
-
-        finally:
-            pass #stage.destroy()
+                # Now try to fetch each package.
+                for name, mock_repo in self.repos.items():
+                    spec = Spec(name).concretized()
+                    pkg = spec.package
+
+                    saved_checksum_setting = spack.do_checksum
+                    with pkg.stage:
+                        # Stage the archive from the mirror and cd to it.
+                        spack.do_checksum = False
+                        pkg.do_stage(mirror_only=True)
+                        # Compare the original repo with the expanded archive
+                        original_path = mock_repo.path
+                        if 'svn' in name:
+                            # have to check out the svn repo to compare.
+                            original_path = join_path(mock_repo.path, 'checked_out')
+                            svn('checkout', mock_repo.url, original_path)
+                        dcmp = dircmp(original_path, pkg.stage.source_path)
+                        # make sure there are no new files in the expanded tarball
+                        self.assertFalse(dcmp.right_only)
+                        # and that all original files are present.
+                        self.assertTrue(all(l in exclude for l in dcmp.left_only))
+                        spack.do_checksum = saved_checksum_setting
 
 
     def test_git_mirror(self):
diff --git a/lib/spack/spack/test/mock_packages_test.py b/lib/spack/spack/test/mock_packages_test.py
index bc1735efe6..079cbcc136 100644
--- a/lib/spack/spack/test/mock_packages_test.py
+++ b/lib/spack/spack/test/mock_packages_test.py
@@ -22,17 +22,15 @@
 # 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 unittest
 import tempfile
-from ordereddict_backport import OrderedDict
-
-from llnl.util.filesystem import mkdirp
+import unittest
 
 import spack
 import spack.config
+from llnl.util.filesystem import mkdirp
+from ordereddict_backport import OrderedDict
 from spack.repository import RepoPath
 from spack.spec import Spec
 
diff --git a/lib/spack/spack/test/mock_repo.py b/lib/spack/spack/test/mock_repo.py
index 9738ba4e72..a8bdfb5571 100644
--- a/lib/spack/spack/test/mock_repo.py
+++ b/lib/spack/spack/test/mock_repo.py
@@ -26,13 +26,9 @@ import os
 import shutil
 
 from llnl.util.filesystem import *
-
-import spack
-from spack.version import ver
 from spack.stage import Stage
 from spack.util.executable import which
 
-
 #
 # VCS Systems used by mock repo code.
 #
@@ -55,6 +51,12 @@ class MockRepo(object):
         mkdirp(self.path)
 
 
+    def destroy(self):
+        """Destroy resources associated with this mock repo."""
+        if self.stage:
+            self.stage.destroy()
+
+
 class MockArchive(MockRepo):
     """Creates a very simple archive directory with a configure script and a
        makefile that installs to a prefix.  Tars it up into an archive."""
diff --git a/lib/spack/spack/test/multimethod.py b/lib/spack/spack/test/multimethod.py
index 7bf4ff0a0a..2d4b8cd584 100644
--- a/lib/spack/spack/test/multimethod.py
+++ b/lib/spack/spack/test/multimethod.py
@@ -25,14 +25,11 @@
 """
 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 *
 
 
 class MultiMethodTest(MockPackagesTest):
diff --git a/lib/spack/spack/test/namespace_trie.py b/lib/spack/spack/test/namespace_trie.py
index d0d809004d..2023ba6d96 100644
--- a/lib/spack/spack/test/namespace_trie.py
+++ b/lib/spack/spack/test/namespace_trie.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
@@ -23,6 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import unittest
+
 from spack.util.naming import NamespaceTrie
 
 
diff --git a/lib/spack/spack/test/optional_deps.py b/lib/spack/spack/test/optional_deps.py
index ebd7281999..55f35ea4c9 100644
--- a/lib/spack/spack/test/optional_deps.py
+++ b/lib/spack/spack/test/optional_deps.py
@@ -22,10 +22,8 @@
 # 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 spack
-from spack.spec import Spec, CompilerSpec
+from spack.spec import Spec
 from spack.test.mock_packages_test import *
 
 class ConcretizeTest(MockPackagesTest):
diff --git a/lib/spack/spack/test/packages.py b/lib/spack/spack/test/packages.py
index 83984dc5f6..f0b5e05f3b 100644
--- a/lib/spack/spack/test/packages.py
+++ b/lib/spack/spack/test/packages.py
@@ -22,14 +22,12 @@
 # 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 llnl.util.filesystem import join_path
 
 import spack
+from llnl.util.filesystem import join_path
 from spack.repository import Repo
-from spack.util.naming import mod_to_class
 from spack.test.mock_packages_test import *
+from spack.util.naming import mod_to_class
 
 
 class PackagesTest(MockPackagesTest):
diff --git a/lib/spack/spack/test/pattern.py b/lib/spack/spack/test/pattern.py
new file mode 100644
index 0000000000..6c783c6a5f
--- /dev/null
+++ b/lib/spack/spack/test/pattern.py
@@ -0,0 +1,104 @@
+##############################################################################
+# 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 unittest
+
+import spack.util.pattern as pattern
+
+
+class CompositeTest(unittest.TestCase):
+
+    def setUp(self):
+        class Base:
+            counter = 0
+
+            def add(self):
+                raise NotImplemented('add not implemented')
+
+            def subtract(self):
+                raise NotImplemented('subtract not implemented')
+
+        class One(Base):
+            def add(self):
+                Base.counter += 1
+
+            def subtract(self):
+                Base.counter -= 1
+
+        class Two(Base):
+            def add(self):
+                Base.counter += 2
+
+            def subtract(self):
+                Base.counter -= 2
+
+        self.Base = Base
+        self.One = One
+        self.Two = Two
+
+    def test_composite_from_method_list(self):
+
+        @pattern.composite(method_list=['add', 'subtract'])
+        class CompositeFromMethodList:
+            pass
+
+        composite = CompositeFromMethodList()
+        composite.append(self.One())
+        composite.append(self.Two())
+        composite.add()
+        self.assertEqual(self.Base.counter, 3)
+        composite.pop()
+        composite.subtract()
+        self.assertEqual(self.Base.counter, 2)
+
+    def test_composite_from_interface(self):
+
+        @pattern.composite(interface=self.Base)
+        class CompositeFromInterface:
+            pass
+
+        composite = CompositeFromInterface()
+        composite.append(self.One())
+        composite.append(self.Two())
+        composite.add()
+        self.assertEqual(self.Base.counter, 3)
+        composite.pop()
+        composite.subtract()
+        self.assertEqual(self.Base.counter, 2)
+
+    def test_error_conditions(self):
+
+        def wrong_container():
+            @pattern.composite(interface=self.Base, container=2)
+            class CompositeFromInterface:
+                pass
+
+        def no_methods():
+            @pattern.composite()
+            class CompositeFromInterface:
+                pass
+
+        self.assertRaises(TypeError, wrong_container)
+        self.assertRaises(TypeError, no_methods)
diff --git a/lib/spack/spack/test/python_version.py b/lib/spack/spack/test/python_version.py
index d74d3b9b7d..4294975304 100644
--- a/lib/spack/spack/test/python_version.py
+++ b/lib/spack/spack/test/python_version.py
@@ -28,12 +28,11 @@ This test ensures that all Spack files are Python version 2.6 or less.
 Spack was originally 2.7, but enough systems in 2014 are still using
 2.6 on their frontend nodes that we need 2.6 to get adopted.
 """
-import unittest
 import os
 import re
+import unittest
 
 import llnl.util.tty as tty
-
 import pyqver2
 import spack
 
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index 632f777cde..5e6162b6e6 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -31,8 +31,6 @@ 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 *
 
diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py
index 44a09cbd7f..8c33d1ff6e 100644
--- a/lib/spack/spack/test/spec_semantics.py
+++ b/lib/spack/spack/test/spec_semantics.py
@@ -22,7 +22,6 @@
 # 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 *
 
diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py
index 1daaa4be8f..6e08e30e13 100644
--- a/lib/spack/spack/test/spec_syntax.py
+++ b/lib/spack/spack/test/spec_syntax.py
@@ -23,9 +23,10 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import unittest
+
 import spack.spec
-from spack.spec import *
 from spack.parse import Token
+from spack.spec import *
 
 # Sample output for a complex lexing.
 complex_lex = [Token(ID, 'mvapich_foo'),
diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py
index c1b2a2a573..dbcf89d864 100644
--- a/lib/spack/spack/test/stage.py
+++ b/lib/spack/spack/test/stage.py
@@ -25,15 +25,13 @@
 """\
 Test that the Stage class works correctly.
 """
-import unittest
-import shutil
 import os
-import getpass
+import shutil
+import unittest
 from contextlib import *
 
-from llnl.util.filesystem import *
-
 import spack
+from llnl.util.filesystem import *
 from spack.stage import Stage
 from spack.util.executable import which
 
@@ -192,116 +190,90 @@ class StageTest(unittest.TestCase):
 
     def test_setup_and_destroy_name_with_tmp(self):
         with use_tmp(True):
-            stage = Stage(archive_url, name=stage_name)
-            self.check_setup(stage, stage_name)
-
-            stage.destroy()
+            with Stage(archive_url, name=stage_name) as stage:
+                self.check_setup(stage, stage_name)
             self.check_destroy(stage, stage_name)
 
 
     def test_setup_and_destroy_name_without_tmp(self):
         with use_tmp(False):
-            stage = Stage(archive_url, name=stage_name)
-            self.check_setup(stage, stage_name)
-
-            stage.destroy()
+            with Stage(archive_url, name=stage_name) as stage:
+                self.check_setup(stage, stage_name)
             self.check_destroy(stage, stage_name)
 
 
     def test_setup_and_destroy_no_name_with_tmp(self):
         with use_tmp(True):
-            stage = Stage(archive_url)
-            self.check_setup(stage, None)
-
-            stage.destroy()
+            with Stage(archive_url) as stage:
+                self.check_setup(stage, None)
             self.check_destroy(stage, None)
 
 
     def test_setup_and_destroy_no_name_without_tmp(self):
         with use_tmp(False):
-            stage = Stage(archive_url)
-            self.check_setup(stage, None)
-
-            stage.destroy()
+            with Stage(archive_url) as stage:
+                self.check_setup(stage, None)
             self.check_destroy(stage, None)
 
 
     def test_chdir(self):
-        stage = Stage(archive_url, name=stage_name)
-
-        stage.chdir()
-        self.check_setup(stage, stage_name)
-        self.check_chdir(stage, stage_name)
-
-        stage.destroy()
+        with Stage(archive_url, name=stage_name) as stage:
+            stage.chdir()
+            self.check_setup(stage, stage_name)
+            self.check_chdir(stage, stage_name)
         self.check_destroy(stage, stage_name)
 
 
     def test_fetch(self):
-        stage = Stage(archive_url, name=stage_name)
-
-        stage.fetch()
-        self.check_setup(stage, stage_name)
-        self.check_chdir(stage, stage_name)
-        self.check_fetch(stage, stage_name)
-
-        stage.destroy()
+        with Stage(archive_url, name=stage_name) as stage:
+            stage.fetch()
+            self.check_setup(stage, stage_name)
+            self.check_chdir(stage, stage_name)
+            self.check_fetch(stage, stage_name)
         self.check_destroy(stage, stage_name)
 
 
     def test_expand_archive(self):
-        stage = Stage(archive_url, name=stage_name)
-
-        stage.fetch()
-        self.check_setup(stage, stage_name)
-        self.check_fetch(stage, stage_name)
-
-        stage.expand_archive()
-        self.check_expand_archive(stage, stage_name)
-
-        stage.destroy()
+        with Stage(archive_url, name=stage_name) as stage:
+            stage.fetch()
+            self.check_setup(stage, stage_name)
+            self.check_fetch(stage, stage_name)
+            stage.expand_archive()
+            self.check_expand_archive(stage, stage_name)
         self.check_destroy(stage, stage_name)
 
 
     def test_expand_archive(self):
-        stage = Stage(archive_url, name=stage_name)
-
-        stage.fetch()
-        self.check_setup(stage, stage_name)
-        self.check_fetch(stage, stage_name)
-
-        stage.expand_archive()
-        stage.chdir_to_source()
-        self.check_expand_archive(stage, stage_name)
-        self.check_chdir_to_source(stage, stage_name)
-
-        stage.destroy()
+        with Stage(archive_url, name=stage_name) as stage:
+            stage.fetch()
+            self.check_setup(stage, stage_name)
+            self.check_fetch(stage, stage_name)
+            stage.expand_archive()
+            stage.chdir_to_source()
+            self.check_expand_archive(stage, stage_name)
+            self.check_chdir_to_source(stage, stage_name)
         self.check_destroy(stage, stage_name)
 
 
     def test_restage(self):
-        stage = Stage(archive_url, name=stage_name)
-
-        stage.fetch()
-        stage.expand_archive()
-        stage.chdir_to_source()
-        self.check_expand_archive(stage, stage_name)
-        self.check_chdir_to_source(stage, stage_name)
-
-        # Try to make a file in the old archive dir
-        with open('foobar', 'w') as file:
-            file.write("this file is to be destroyed.")
-
-        self.assertTrue('foobar' in os.listdir(stage.source_path))
-
-        # Make sure the file is not there after restage.
-        stage.restage()
-        self.check_chdir(stage, stage_name)
-        self.check_fetch(stage, stage_name)
-
-        stage.chdir_to_source()
-        self.check_chdir_to_source(stage, stage_name)
-        self.assertFalse('foobar' in os.listdir(stage.source_path))
-
-        stage.destroy()
+        with Stage(archive_url, name=stage_name) as stage:
+            stage.fetch()
+            stage.expand_archive()
+            stage.chdir_to_source()
+            self.check_expand_archive(stage, stage_name)
+            self.check_chdir_to_source(stage, stage_name)
+
+            # Try to make a file in the old archive dir
+            with open('foobar', 'w') as file:
+                file.write("this file is to be destroyed.")
+
+            self.assertTrue('foobar' in os.listdir(stage.source_path))
+
+            # Make sure the file is not there after restage.
+            stage.restage()
+            self.check_chdir(stage, stage_name)
+            self.check_fetch(stage, stage_name)
+            stage.chdir_to_source()
+            self.check_chdir_to_source(stage, stage_name)
+            self.assertFalse('foobar' in os.listdir(stage.source_path))
         self.check_destroy(stage, stage_name)
diff --git a/lib/spack/spack/test/svn_fetch.py b/lib/spack/spack/test/svn_fetch.py
index 7d150b42f4..1ee4ee700e 100644
--- a/lib/spack/spack/test/svn_fetch.py
+++ b/lib/spack/spack/test/svn_fetch.py
@@ -24,18 +24,12 @@
 ##############################################################################
 import os
 import re
-import unittest
-import shutil
-import tempfile
-
-from llnl.util.filesystem import *
-
 import spack
+
+from spack.test.mock_repo import svn, MockSvnRepo
 from spack.version import ver
-from spack.stage import Stage
-from spack.util.executable import which
 from spack.test.mock_packages_test import *
-from spack.test.mock_repo import svn, MockSvnRepo
+from llnl.util.filesystem import *
 
 
 class SvnFetchTest(MockPackagesTest):
@@ -51,16 +45,10 @@ class SvnFetchTest(MockPackagesTest):
         spec.concretize()
         self.pkg = spack.repo.get(spec, new=True)
 
-
     def tearDown(self):
         """Destroy the stage space used by this test."""
         super(SvnFetchTest, self).tearDown()
-
-        if self.repo.stage is not None:
-            self.repo.stage.destroy()
-
-        self.pkg.do_clean()
-
+        self.repo.destroy()
 
     def assert_rev(self, rev):
         """Check that the current revision is equal to the supplied rev."""
@@ -73,7 +61,6 @@ class SvnFetchTest(MockPackagesTest):
                     return match.group(1)
         self.assertEqual(get_rev(), rev)
 
-
     def try_fetch(self, rev, test_file, args):
         """Tries to:
            1. Fetch the repo using a fetch strategy constructed with
@@ -85,26 +72,27 @@ class SvnFetchTest(MockPackagesTest):
         """
         self.pkg.versions[ver('svn')] = args
 
-        self.pkg.do_stage()
-        self.assert_rev(rev)
+        with self.pkg.stage:
+            self.pkg.do_stage()
+            self.assert_rev(rev)
 
-        file_path = join_path(self.pkg.stage.source_path, test_file)
-        self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
-        self.assertTrue(os.path.isfile(file_path))
+            file_path = join_path(self.pkg.stage.source_path, test_file)
+            self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
+            self.assertTrue(os.path.isfile(file_path))
 
-        os.unlink(file_path)
-        self.assertFalse(os.path.isfile(file_path))
+            os.unlink(file_path)
+            self.assertFalse(os.path.isfile(file_path))
 
-        untracked = 'foobarbaz'
-        touch(untracked)
-        self.assertTrue(os.path.isfile(untracked))
-        self.pkg.do_restage()
-        self.assertFalse(os.path.isfile(untracked))
+            untracked = 'foobarbaz'
+            touch(untracked)
+            self.assertTrue(os.path.isfile(untracked))
+            self.pkg.do_restage()
+            self.assertFalse(os.path.isfile(untracked))
 
-        self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
-        self.assertTrue(os.path.isfile(file_path))
+            self.assertTrue(os.path.isdir(self.pkg.stage.source_path))
+            self.assertTrue(os.path.isfile(file_path))
 
-        self.assert_rev(rev)
+            self.assert_rev(rev)
 
 
     def test_fetch_default(self):
diff --git a/lib/spack/spack/test/tally_plugin.py b/lib/spack/spack/test/tally_plugin.py
index 9ca898c47c..4163ab95dd 100644
--- a/lib/spack/spack/test/tally_plugin.py
+++ b/lib/spack/spack/test/tally_plugin.py
@@ -6,7 +6,7 @@
 # Written 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://scalability-software.llnl.gov/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
@@ -22,10 +22,10 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-from nose.plugins import Plugin
-
 import os
 
+from nose.plugins import Plugin
+
 class Tally(Plugin):
     name = 'tally'
 
@@ -34,7 +34,7 @@ class Tally(Plugin):
         self.successCount = 0
         self.failCount = 0
         self.errorCount = 0
-    
+
     @property
     def numberOfTestsRun(self):
         """Excludes skipped tests"""
@@ -48,10 +48,10 @@ class Tally(Plugin):
 
     def addSuccess(self, test):
         self.successCount += 1
-        
+
     def addError(self, test, err):
         self.errorCount += 1
-            
+
     def addFailure(self, test, err):
         self.failCount += 1
 
diff --git a/lib/spack/spack/test/unit_install.py b/lib/spack/spack/test/unit_install.py
index ccc409dd60..18615b7efe 100644
--- a/lib/spack/spack/test/unit_install.py
+++ b/lib/spack/spack/test/unit_install.py
@@ -22,10 +22,11 @@
 # 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 itertools
+import unittest
 
 import spack
+
 test_install = __import__("spack.cmd.test-install",
     fromlist=["BuildId", "create_test_output", "TestResult"])
 
diff --git a/lib/spack/spack/test/url_extrapolate.py b/lib/spack/spack/test/url_extrapolate.py
index 87adf89401..068a335b49 100644
--- a/lib/spack/spack/test/url_extrapolate.py
+++ b/lib/spack/spack/test/url_extrapolate.py
@@ -25,10 +25,7 @@
 """\
 Tests ability of spack to extrapolate URL versions from existing versions.
 """
-import spack
 import spack.url as url
-from spack.spec import Spec
-from spack.version import ver
 from spack.test.mock_packages_test import *
 
 
diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py
index efde7c0c73..561d4658a1 100644
--- a/lib/spack/spack/test/url_parse.py
+++ b/lib/spack/spack/test/url_parse.py
@@ -27,8 +27,8 @@ This file has a bunch of versions tests taken from the excellent version
 detection in Homebrew.
 """
 import unittest
+
 import spack.url as url
-from pprint import pprint
 
 
 class UrlParseTest(unittest.TestCase):
diff --git a/lib/spack/spack/test/url_substitution.py b/lib/spack/spack/test/url_substitution.py
index aec8baf4ea..2be38af0d3 100644
--- a/lib/spack/spack/test/url_substitution.py
+++ b/lib/spack/spack/test/url_substitution.py
@@ -27,7 +27,6 @@ This test does sanity checks on substituting new versions into URLs
 """
 import unittest
 
-import spack
 import spack.url as url
 
 
diff --git a/lib/spack/spack/test/versions.py b/lib/spack/spack/test/versions.py
index 108450e098..2732006eb3 100644
--- a/lib/spack/spack/test/versions.py
+++ b/lib/spack/spack/test/versions.py
@@ -28,6 +28,7 @@ We try to maintain compatibility with RPM's version semantics
 where it makes sense.
 """
 import unittest
+
 from spack.version import *
 
 
diff --git a/lib/spack/spack/test/yaml.py b/lib/spack/spack/test/yaml.py
index 5a357b8e69..b930c022f2 100644
--- a/lib/spack/spack/test/yaml.py
+++ b/lib/spack/spack/test/yaml.py
@@ -26,6 +26,7 @@
 Test Spack's custom YAML format.
 """
 import unittest
+
 import spack.util.spack_yaml as syaml
 
 test_file = """\
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
index 02c0b83e26..ad551a6ded 100644
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -225,7 +225,7 @@ def parse_version_offset(path):
         (r'_((\d+\.)+\d+[a-z]?)[.]orig$', stem),
 
         # e.g. http://www.openssl.org/source/openssl-0.9.8s.tar.gz
-        (r'-([^-]+(-alpha|-beta)?)', stem),
+        (r'-v?([^-]+(-alpha|-beta)?)', stem),
 
         # e.g. astyle_1.23_macosx.tar.gz
         (r'_([^_]+(_alpha|_beta)?)', stem),
diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py
index cd413dcfbc..ae8e5708be 100644
--- a/lib/spack/spack/util/environment.py
+++ b/lib/spack/spack/util/environment.py
@@ -63,3 +63,10 @@ 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()):
+            env_file.write("%s=%s\n" % (key, val))
diff --git a/lib/spack/spack/util/pattern.py b/lib/spack/spack/util/pattern.py
new file mode 100644
index 0000000000..17a126498b
--- /dev/null
+++ b/lib/spack/spack/util/pattern.py
@@ -0,0 +1,116 @@
+##############################################################################
+# 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 inspect
+import collections
+import functools
+
+
+def composite(interface=None, method_list=None, container=list):
+    """
+    Returns a class decorator that patches a class adding all the methods it needs to be a composite for a given
+    interface.
+
+    :param interface: class exposing the interface to which the composite object must conform. Only non-private and
+    non-special methods will be taken into account
+
+    :param method_list: names of methods that should be part of the composite
+
+    :param container: container for the composite object (default = list). Must fulfill the MutableSequence contract.
+    The composite class will expose the container API to manage object composition
+
+    :return: class decorator
+    """
+    # Check if container fulfills the MutableSequence contract and raise an exception if it doesn't
+    # The patched class returned by the decorator will inherit from the container class to expose the
+    # interface needed to manage objects composition
+    if not issubclass(container, collections.MutableSequence):
+        raise TypeError("Container must fulfill the MutableSequence contract")
+
+    # Check if at least one of the 'interface' or the 'method_list' arguments are defined
+    if interface is None and method_list is None:
+        raise TypeError("Either 'interface' or 'method_list' must be defined on a call to composite")
+
+    def cls_decorator(cls):
+        # Retrieve the base class of the composite. Inspect its methods and decide which ones will be overridden
+        def no_special_no_private(x):
+            return inspect.ismethod(x) and not x.__name__.startswith('_')
+
+        # Patch the behavior of each of the methods in the previous list. This is done associating an instance of the
+        # descriptor below to any method that needs to be patched.
+        class IterateOver(object):
+            """
+            Decorator used to patch methods in a composite. It iterates over all the items in the instance containing the
+            associated attribute and calls for each of them an attribute with the same name
+            """
+            def __init__(self, name, func=None):
+                self.name = name
+                self.func = func
+
+            def __get__(self, instance, owner):
+                def getter(*args, **kwargs):
+                    for item in instance:
+                        getattr(item, self.name)(*args, **kwargs)
+                # If we are using this descriptor to wrap a method from an interface, then we must conditionally
+                # use the `functools.wraps` decorator to set the appropriate fields.
+                if self.func is not None:
+                    getter = functools.wraps(self.func)(getter)
+                return getter
+
+        dictionary_for_type_call = {}
+        # Construct a dictionary with the methods explicitly passed as name
+        if method_list is not None:
+            # python@2.7: method_list_dict = {name: IterateOver(name) for name in method_list}
+            method_list_dict = {}
+            for name in method_list:
+                method_list_dict[name] = IterateOver(name)
+            dictionary_for_type_call.update(method_list_dict)
+        # Construct a dictionary with the methods inspected from the interface
+        if interface is not None:
+            ##########
+            # python@2.7: interface_methods = {name: method for name, method in inspect.getmembers(interface, predicate=no_special_no_private)}
+            interface_methods = {}
+            for name, method in inspect.getmembers(interface, predicate=no_special_no_private):
+                interface_methods[name] = method
+            ##########
+            # python@2.7: interface_methods_dict = {name: IterateOver(name, method) for name, method in interface_methods.iteritems()}
+            interface_methods_dict = {}
+            for name, method in interface_methods.iteritems():
+                interface_methods_dict[name] = IterateOver(name, method)
+            ##########
+            dictionary_for_type_call.update(interface_methods_dict)
+        # Get the methods that are defined in the scope of the composite class and override any previous definition
+        ##########
+        # python@2.7: cls_method = {name: method for name, method in inspect.getmembers(cls, predicate=inspect.ismethod)}
+        cls_method = {}
+        for name, method in inspect.getmembers(cls, predicate=inspect.ismethod):
+            cls_method[name] = method
+        ##########
+        dictionary_for_type_call.update(cls_method)
+        # Generate the new class on the fly and return it
+        # FIXME : inherit from interface if we start to use ABC classes?
+        wrapper_class = type(cls.__name__, (cls, container), dictionary_for_type_call)
+        return wrapper_class
+
+    return cls_decorator
diff --git a/lib/spack/spack/util/web.py b/lib/spack/spack/util/web.py
index e26daef296..73f4858b02 100644
--- a/lib/spack/spack/util/web.py
+++ b/lib/spack/spack/util/web.py
@@ -86,12 +86,12 @@ def _spider(args):
 
         if not "Content-type" in resp.headers:
             tty.debug("ignoring page " + url)
-            return pages
+            return pages, links
 
         if not resp.headers["Content-type"].startswith('text/html'):
             tty.debug("ignoring page " + url + " with content type " +
                       resp.headers["Content-type"])
-            return pages
+            return pages, links
 
         # Do the real GET request when we know it's just HTML.
         req.get_method = lambda: "GET"
@@ -173,7 +173,7 @@ def spider(root_url, **kwargs):
        performance over a sequential fetch.
     """
     max_depth = kwargs.setdefault('depth', 1)
-    pages, links =  _spider((root_url, set(), root_url, None, 1, max_depth, False))
+    pages, links = _spider((root_url, set(), root_url, None, 1, max_depth, False))
     return pages, links
 
 
diff --git a/var/spack/repos/builtin/packages/SuiteSparse/package.py b/var/spack/repos/builtin/packages/SuiteSparse/package.py
new file mode 100644
index 0000000000..6e130d118f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/SuiteSparse/package.py
@@ -0,0 +1,27 @@
+from spack import *
+
+
+class Suitesparse(Package):
+    """
+    SuiteSparse is a suite of sparse matrix algorithms
+    """
+    homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html'
+    url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz'
+
+    version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
+
+    depends_on('blas')
+    depends_on('lapack')
+
+    depends_on('metis@5.1.0', when='@4.5.1')
+
+    def install(self, spec, prefix):
+        # The build system of SuiteSparse is quite old-fashioned
+        # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk)
+        # with a lot of convoluted logic in it.
+        # Any kind of customization will need to go through filtering of that file
+
+        # FIXME : this actually uses the current workaround
+        # FIXME : (blas / lapack always provide libblas and liblapack as aliases)
+        make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack')
+
diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
new file mode 100644
index 0000000000..0b49d14202
--- /dev/null
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -0,0 +1,57 @@
+from spack import *
+
+
+class ArpackNg(Package):
+    """
+    ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
+
+    Important Features:
+
+    * Reverse Communication Interface.
+    * Single and Double Precision Real Arithmetic Versions for Symmetric,
+      Non-symmetric, Standard or Generalized Problems.
+    * Single and Double Precision Complex Arithmetic Versions for Standard or
+      Generalized Problems.
+    * Routines for Banded Matrices - Standard or Generalized Problems.
+    * Routines for The Singular Value Decomposition.
+    * Example driver routines that may be used as templates to implement numerous
+      Shift-Invert strategies for all problem types, data types and precision.
+
+    This project is a joint project between Debian, Octave and Scilab in order to
+    provide a common and maintained version of arpack.
+
+    Indeed, no single release has been published by Rice university for the last
+    few years and since many software (Octave, Scilab, R, Matlab...) forked it and
+    implemented their own modifications, arpack-ng aims to tackle this by providing
+    a common repository and maintained versions.
+
+    arpack-ng is replacing arpack almost everywhere.
+    """
+    homepage = 'https://github.com/opencollab/arpack-ng'
+    url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz'
+
+    version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5')
+
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('mpi', default=False, description='Activates MPI support')
+
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('mpi', when='+mpi')
+
+    def install(self, spec, prefix):
+        # Apparently autotools are not bootstrapped
+        bootstrap = Executable('./bootstrap')
+
+        options = ['--prefix=%s' % prefix]
+
+        if '+mpi' in spec:
+            options.append('--enable-mpi')
+
+        if '~shared' in spec:
+            options.append('--enable-shared=no')
+
+        bootstrap()
+        configure(*options)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py
index 5189faf054..6412e810a6 100644
--- a/var/spack/repos/builtin/packages/autoconf/package.py
+++ b/var/spack/repos/builtin/packages/autoconf/package.py
@@ -6,6 +6,7 @@ class Autoconf(Package):
     url      = "http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz"
 
     version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
+    version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py
index 9115822730..2172a42030 100644
--- a/var/spack/repos/builtin/packages/automake/package.py
+++ b/var/spack/repos/builtin/packages/automake/package.py
@@ -5,7 +5,9 @@ class Automake(Package):
     homepage = "http://www.gnu.org/software/automake/"
     url      = "http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz"
 
+    version('1.15',   '716946a105ca228ab545fc37a70df3a3')
     version('1.14.1', 'd052a3e884631b9c7892f2efce542d75')
+    version('1.11.6', '0286dc30295b62985ca51919202ecfcc')
 
     depends_on('autoconf')
 
diff --git a/var/spack/repos/builtin/packages/blitz/package.py b/var/spack/repos/builtin/packages/blitz/package.py
new file mode 100644
index 0000000000..9413b276fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blitz/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class Blitz(Package):
+    """N-dimensional arrays for C++"""
+    homepage = "http://github.com/blitzpp/blitz"
+    url      = "https://github.com/blitzpp/blitz/tarball/1.0.0"
+
+    version('1.0.0', '9f040b9827fe22228a892603671a77af')
+
+    # No dependencies
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/boost/boost_11856.patch b/var/spack/repos/builtin/packages/boost/boost_11856.patch
new file mode 100644
index 0000000000..3b4052ca18
--- /dev/null
+++ b/var/spack/repos/builtin/packages/boost/boost_11856.patch
@@ -0,0 +1,34 @@
+--- a/libs/container/src/pool_resource.cpp	2015-11-06 12:49:55.000000000 -0800
++++ b/libs/container/src/pool_resource.cpp	2015-12-22 07:54:36.202131121 -0800
+@@ -32,11 +32,11 @@
+ class pool_data_t
+    : public block_slist_base<>
+ {
+-   typedef block_slist_base<> block_slist_base;
++   typedef block_slist_base<> block_slist_base_t;
+ 
+    public:
+    explicit pool_data_t(std::size_t initial_blocks_per_chunk)
+-      : block_slist_base(), next_blocks_per_chunk(initial_blocks_per_chunk)
++      : block_slist_base_t(), next_blocks_per_chunk(initial_blocks_per_chunk)
+    {  slist_algo::init_header(&free_slist);  }
+ 
+    void *allocate_block() BOOST_NOEXCEPT
+@@ -59,7 +59,7 @@
+    void release(memory_resource &upstream)
+    {
+       slist_algo::init_header(&free_slist);
+-      this->block_slist_base::release(upstream);
++      this->block_slist_base_t::release(upstream);
+       next_blocks_per_chunk = pool_options_minimum_max_blocks_per_chunk;
+    }
+ 
+@@ -72,7 +72,7 @@
+       
+       //Minimum block size is at least max_align, so all pools allocate sizes that are multiple of max_align,
+       //meaning that all blocks are max_align-aligned.
+-      char *p = static_cast<char *>(block_slist_base::allocate(blocks_per_chunk*pool_block, mr));
++      char *p = static_cast<char *>(block_slist_base_t::allocate(blocks_per_chunk*pool_block, mr));
+ 
+       //Create header types. This is no-throw
+       for(std::size_t i = 0, max = blocks_per_chunk; i != max; ++i){
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 3427b74ad6..fb1f5daee7 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import spack
 
 class Boost(Package):
     """Boost provides free peer-reviewed portable C++ source
@@ -44,15 +45,50 @@ class Boost(Package):
     version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5')
     version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
 
+    default_install_libs = set(['atomic', 
+        'chrono', 
+        'date_time', 
+        'filesystem', 
+        'graph',
+        'iostreams',
+        'locale',
+        'log',
+        'math', 
+        'program_options',
+        'random', 
+        'regex', 
+        'serialization', 
+        'signals', 
+        'system', 
+        'test', 
+        'thread', 
+        'wave'])
+
+    # mpi/python are not installed by default because they pull in many 
+    # dependencies and/or because there is a great deal of customization 
+    # possible (and it would be difficult to choose sensible defaults)
+    default_noinstall_libs = set(['mpi', 'python'])
+
+    all_libs = default_install_libs | default_noinstall_libs
+
+    for lib in all_libs:
+        variant(lib, default=(lib not in default_noinstall_libs), 
+            description="Compile with {0} library".format(lib))
+
     variant('debug', default=False, description='Switch to the debug version of Boost')
-    variant('python', default=False, description='Activate the component Boost.Python')
-    variant('mpi', default=False, description='Activate the component Boost.MPI')
-    variant('compression', default=True, description='Activate the compression Boost.iostreams')
+    variant('shared', default=True, description="Additionally build shared libraries")
+    variant('multithreaded', default=True, description="Build multi-threaded versions of libraries")
+    variant('singlethreaded', default=True, description="Build single-threaded versions of libraries")
+    variant('icu_support', default=False, description="Include ICU support (for regex/locale libraries)")
 
+    depends_on('icu', when='+icu_support')
     depends_on('python', when='+python')
     depends_on('mpi', when='+mpi')
-    depends_on('bzip2', when='+compression')
-    depends_on('zlib', when='+compression')
+    depends_on('bzip2', when='+iostreams')
+    depends_on('zlib', when='+iostreams')
+
+    # Patch fix from https://svn.boost.org/trac/boost/ticket/11856
+    patch('boost_11856.patch', when='@1.60.0%gcc@4.4.7')
 
     def url_for_version(self, version):
         """Handle Boost's weird URLs, which write the version two different ways."""
@@ -77,22 +113,20 @@ class Boost(Package):
         # fallback to gcc if no toolset found
         return 'gcc'
 
-    def determine_bootstrap_options(self, spec, options):
-        options.append('--with-toolset=%s' % self.determine_toolset(spec))
+    def determine_bootstrap_options(self, spec, withLibs, options):
+        boostToolsetId = self.determine_toolset(spec)
+        options.append('--with-toolset=%s' % boostToolsetId)
+        options.append("--with-libraries=%s" % ','.join(withLibs))
 
-        without_libs = []
-        if '~mpi' in spec:
-            without_libs.append('mpi')
-        if '~python' in spec:
-            without_libs.append('python')
-        else:
+        if '+python' in spec:
             options.append('--with-python=%s' %
                 join_path(spec['python'].prefix.bin, 'python'))
 
-        if without_libs:
-            options.append('--without-libraries=%s' % ','.join(without_libs))
-
         with open('user-config.jam', 'w') as f:
+            compiler_wrapper = join_path(spack.build_env_path, 'c++')
+            f.write("using {0} : : {1} ;\n".format(boostToolsetId, 
+                compiler_wrapper))
+            
             if '+mpi' in spec:
                 f.write('using mpi : %s ;\n' %
                     join_path(spec['mpi'].prefix.bin, 'mpicxx'))
@@ -107,12 +141,10 @@ class Boost(Package):
         else:
             options.append('variant=release')
 
-        if '~compression' in spec:
-            options.extend([
-                '-s', 'NO_BZIP2=1',
-                '-s', 'NO_ZLIB=1'])
+        if '+icu_support' in spec:
+            options.extend(['-s', 'ICU_PATH=%s' % spec['icu'].prefix])
 
-        if '+compression' in spec:
+        if '+iostreams' in spec:
             options.extend([
                 '-s', 'BZIP2_INCLUDE=%s' % spec['bzip2'].prefix.include,
                 '-s', 'BZIP2_LIBPATH=%s' % spec['bzip2'].prefix.lib,
@@ -120,20 +152,46 @@ class Boost(Package):
                 '-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib,
                 ])
 
+        linkTypes = ['static']
+        if '+shared' in spec:
+            linkTypes.append('shared')
+        
+        threadingOpts = []
+        if '+multithreaded' in spec:
+            threadingOpts.append('multi')
+        if '+singlethreaded' in spec:
+            threadingOpts.append('single')
+        if not threadingOpts:
+            raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled")
+        
         options.extend([
             'toolset=%s' % self.determine_toolset(spec),
-            'link=static,shared',
-            'threading=single,multi',
+            'link=%s' % ','.join(linkTypes),
             '--layout=tagged'])
+        
+        return threadingOpts
 
     def install(self, spec, prefix):
+        withLibs = list()
+        for lib in Boost.all_libs:
+            if "+{0}".format(lib) in spec:
+                withLibs.append(lib)
+        if not withLibs:
+            # if no libraries are specified for compilation, then you dont have 
+            # to configure/build anything, just copy over to the prefix directory.
+            src = join_path(self.stage.source_path, 'boost')
+            mkdirp(join_path(prefix, 'include'))
+            dst = join_path(prefix, 'include', 'boost')
+            install_tree(src, dst)
+            return
+    
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 
         bootstrap = Executable('./bootstrap.sh')
 
         bootstrap_options = ['--prefix=%s' % prefix]
-        self.determine_bootstrap_options(spec, bootstrap_options)
+        self.determine_bootstrap_options(spec, withLibs, bootstrap_options)
 
         bootstrap(*bootstrap_options)
 
@@ -143,6 +201,10 @@ class Boost(Package):
         b2 = Executable(b2name)
         b2_options = ['-j', '%s' % make_jobs]
 
-        self.determine_b2_options(spec, b2_options)
+        threadingOpts = self.determine_b2_options(spec, b2_options)
 
-        b2('install', *b2_options)
+        # In theory it could be done on one call but it fails on
+        # Boost.MPI if the threading options are not separated.
+        for threadingOpt in threadingOpts:
+            b2('install', 'threading=%s' % threadingOpt, *b2_options)
+        
diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py
new file mode 100644
index 0000000000..d51b4a4dd5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/caliper/package.py
@@ -0,0 +1,25 @@
+from spack import *
+
+class Caliper(Package):
+    """
+    Caliper is a generic context annotation system. It gives programmers the
+    ability to provide arbitrary program context information to (performance)
+    tools at runtime.
+    """
+
+    homepage = "https://github.com/LLNL/Caliper"
+    url      = ""
+
+    version('master', git='ssh://git@github.com:LLNL/Caliper.git')
+
+    variant('mpi', default=False, description='Enable MPI function wrappers.')
+
+    depends_on('libunwind')
+    depends_on('papi')
+    depends_on('mpi', when='+mpi')
+
+    def install(self, spec, prefix):
+      with working_dir('build', create=True):
+        cmake('..', *std_cmake_args)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py
index 97356433be..ef4a2736db 100644
--- a/var/spack/repos/builtin/packages/cgal/package.py
+++ b/var/spack/repos/builtin/packages/cgal/package.py
@@ -46,6 +46,7 @@ class Cgal(Package):
     depends_on('mpfr')
     depends_on('gmp')
     depends_on('zlib')
+    depends_on('cmake')
 
     # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL)
     # FIXME : Optional third party libraries missing
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index f67ae21ebd..e20c1e4aeb 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -28,20 +28,22 @@ class Cmake(Package):
     """A cross-platform, open-source build system. CMake is a family of
        tools designed to build, test and package software."""
     homepage  = 'https://www.cmake.org'
+    url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
 
-    version('2.8.10.2', '097278785da7182ec0aea8769d06860c',
-            url = 'http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz')
-
-    version('3.0.2', 'db4c687a31444a929d2fdc36c4dfb95f',
-            url = 'http://www.cmake.org/files/v3.0/cmake-3.0.2.tar.gz')
-
-    version('3.4.0', 'cd3034e0a44256a0917e254167217fc8',
-            url = 'http://cmake.org/files/v3.4/cmake-3.4.0.tar.gz')
+    version('3.4.3',    '4cb3ff35b2472aae70f542116d616e63')
+    version('3.4.0',    'cd3034e0a44256a0917e254167217fc8')
+    version('3.3.1',    '52638576f4e1e621fed6c3410d3a1b12')
+    version('3.0.2',    'db4c687a31444a929d2fdc36c4dfb95f')
+    version('2.8.10.2', '097278785da7182ec0aea8769d06860c')
 
     variant('ncurses', default=True, description='Enables the build of the ncurses gui')
-
     depends_on('ncurses', when='+ncurses')
 
+    def url_for_version(self, version):
+        """Handle CMake's version-based custom URLs."""
+        return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version)
+
+
     def install(self, spec, prefix):
         configure('--prefix='   + prefix,
                   '--parallel=' + str(make_jobs),
diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py
new file mode 100644
index 0000000000..7377016a6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cmocka/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class Cmocka(Package):
+    """Unit-testing framework in pure C"""
+    homepage = "https://cmocka.org/"
+    url      = "https://cmocka.org/files/1.0/cmocka-1.0.1.tar.xz"
+
+    version('1.0.1', 'ed861e501a21a92b2af63e466df2015e')
+    parallel = False
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+	    cmake('..', *std_cmake_args)
+
+	    make()
+	    make("install")
diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
new file mode 100644
index 0000000000..1693c4b160
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -0,0 +1,31 @@
+import glob
+from spack import *
+
+class Cryptopp(Package):
+    """Crypto++ is an open-source C++ library of cryptographic schemes. The
+       library supports a number of different cryptography algorithms, including
+       authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2),
+       public-key encryption (RSA, DSA), and a few obsolete/historical encryption
+       algorithms (MD5, Panama)."""
+
+    homepage = "http://www.cryptopp.com/"
+    url      = "http://www.cryptopp.com/cryptopp563.zip"
+
+    version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
+    version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
+
+    def install(self, spec, prefix):
+        make()
+
+        mkdirp(prefix.include)
+        for hfile in glob.glob('*.h*'):
+            install(hfile, prefix.include)
+
+        mkdirp(prefix.lib)
+        install('libcryptopp.a', prefix.lib)
+
+    def url_for_version(self, version):
+        version_tuple = tuple(v for v in iter(version))
+        version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "")
+
+        return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string)
diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py
new file mode 100644
index 0000000000..5ec82ef83d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dakota/package.py
@@ -0,0 +1,55 @@
+from spack import *
+
+
+class Dakota(Package):
+    """
+    The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems
+    analysis methods. Dakota contains algorithms for:
+
+    - optimization with gradient and non gradient-based methods;
+    - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods;
+    - parameter estimation with nonlinear least squares methods;
+    - sensitivity/variance analysis with design of experiments and parameter study methods.
+
+    These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization,
+    surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty.
+    """
+
+    homepage = 'https://dakota.sandia.gov/'
+    url = 'https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.3-public.src.tar.gz'
+    _url_str = 'https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-{version}-public.src.tar.gz'
+
+    version('6.3', '05a58d209fae604af234c894c3f73f6d')
+
+    variant('debug', default=False, description='Builds a debug version of the libraries')
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('mpi', default=True, description='Activates MPI support')
+
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('mpi', when='+mpi')
+
+    depends_on('python')
+    depends_on('boost')
+
+    def url_for_version(self, version):
+        return Dakota._url_str.format(version=version)
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+
+        options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                        '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF')])
+
+        if '+mpi' in spec:
+            options.extend(['-DDAKOTA_HAVE_MPI:BOOL=ON',
+                            '-DMPI_CXX_COMPILER:STRING=%s' % join_path(spec['mpi'].prefix.bin, 'mpicxx')])
+
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+
+        with working_dir(build_directory, create=True):
+            cmake(source_directory, *options)
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index 44ee6819f5..e40046b452 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -41,13 +41,14 @@ class Eigen(Package):
     variant('metis', default=True, description='Enables metis backend')
     variant('scotch', default=True, description='Enables scotch backend')
     variant('fftw', default=True, description='Enables FFTW backend')
+    variant('suitesparse', default=True, description='Enables SuiteSparse support')
 
-    # TODO : dependency on SuiteSparse, googlehash, superlu, adolc missing
+    # TODO : dependency on googlehash, superlu, adolc missing
 
     depends_on('metis', when='+metis')
     depends_on('scotch', when='+scotch')
     depends_on('fftw', when='+fftw')
-
+    depends_on('SuiteSparse', when='+suitesparse')
     depends_on('mpfr@2.3.0:')  # Eigen 3.2.7 requires at least 2.3.0
     depends_on('gmp')
 
diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
new file mode 100644
index 0000000000..a2bf58f585
--- /dev/null
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -0,0 +1,65 @@
+from spack import *
+
+import os
+
+class Espresso(Package):
+    """
+    QE is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials
+    modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
+    """
+    homepage = 'http://quantum-espresso.org'
+    url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz'
+
+    version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
+
+    variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support')
+    variant('openmp', default=False, description='Enables openMP support')
+    variant('scalapack', default=True, description='Enables scalapack support')
+    variant('elpa', default=True, description='Use elpa as an eigenvalue solver')
+
+    depends_on('blas')
+    depends_on('lapack')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('fftw~mpi', when='~mpi')
+    depends_on('fftw+mpi', when='+mpi')
+    depends_on('scalapack', when='+scalapack+mpi')  # TODO : + mpi needed to avoid false dependencies installation
+    
+    def check_variants(self, spec):
+        error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
+        if '+scalapack' in spec and '~mpi' in spec:
+            raise RuntimeError(error.format(variant='scalapack'))
+        if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
+            raise RuntimeError(error.format(variant='elpa'))
+
+    def install(self, spec, prefix):
+        self.check_variants(spec)
+
+        options = ['-prefix=%s' % prefix]
+
+        if '+mpi' in spec:
+            options.append('--enable-parallel')
+
+        if '+openmp' in spec:
+            options.append('--enable-openmp')
+
+        if '+scalapack' in spec:
+            options.append('--with-scalapack=yes')
+
+        if '+elpa' in spec:
+            options.append('--with-elpa=yes')
+
+        # Add a list of directories to search
+        search_list = []
+        for name, dependency_spec in spec.dependencies.iteritems():
+            search_list.extend([dependency_spec.prefix.lib,
+                                dependency_spec.prefix.lib64])
+
+        search_list = " ".join(search_list)
+        options.append('LIBDIRS=%s' % search_list)
+        options.append('F90=%s' % os.environ['FC'])
+
+        configure(*options)
+        make('all')
+        make('install')        
+
diff --git a/var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch b/var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch
new file mode 100644
index 0000000000..25355269ca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch
@@ -0,0 +1,12 @@
+diff --git a/cmake-exodus b/cmake-exodus
+index 787fd9d..ed073a2 100755
+--- a/cmake-exodus
++++ b/cmake-exodus
+@@ -1,4 +1,6 @@
+-EXTRA_ARGS=$@
++#!/bin/bash
++
++EXTRA_ARGS=-DSEACASProj_ENABLE_CXX11=OFF
+ 
+ ### Change this to point to the compilers you want to use
+ CC=gcc
diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py
new file mode 100644
index 0000000000..af258b7e6e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/exodusii/package.py
@@ -0,0 +1,49 @@
+from spack import *
+
+# TODO: Add support for a C++11 enabled installation that filters out the
+# TODO: "C++11-Disabled" flag (but only if the spec compiler supports C++11).
+
+# TODO: Add support for parallel installation that uses MPI.
+
+# TODO: Create installation options for NetCDF that support larger page size
+# TODO: suggested by Exodus (see the repository "README" file).
+
+class Exodusii(Package):
+    """Exodus II is a C++/Fortran library developed to store and retrieve data for
+       finite element analyses. It's used for preprocessing (problem definition),
+       postprocessing (results visualization), and data transfer between codes.
+       An Exodus II data file is a random access, machine independent, binary
+       file that is written and read via C, C++, or Fortran API routines."""
+
+    homepage = "https://github.com/gsjaardema/seacas"
+    url      = "https://github.com/gsjaardema/seacas/archive/master.zip"
+
+    version('2016-02-08', git='https://github.com/gsjaardema/seacas.git', commit='dcf3529')
+
+    # TODO: Make this a build dependency once build dependencies are supported
+    # (see: https://github.com/LLNL/spack/pull/378).
+    depends_on('cmake@2.8.7:')
+    depends_on('hdf5~shared~mpi')
+    depends_on('netcdf~mpi')
+
+    patch('exodus-cmake.patch')
+
+    def patch(self):
+        ff = FileFilter('cmake-exodus')
+
+        ff.filter('CMAKE_INSTALL_PREFIX:PATH=${ACCESS}',
+            'CMAKE_INSTALL_PREFIX:PATH=%s' % self.spec.prefix, string=True)
+        ff.filter('NetCDF_DIR:PATH=${TPL}',
+            'NetCDF_DIR:PATH=%s' % self.spec['netcdf'].prefix, string=True)
+        ff.filter('HDF5_ROOT:PATH=${TPL}',
+            'HDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix, string=True)
+
+    def install(self, spec, prefix):
+        mkdirp('build')
+        cd('build')
+
+        cmake_exodus = Executable('../cmake-exodus')
+        cmake_exodus()
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py
index 082da5bf0b..3f925c6546 100644
--- a/var/spack/repos/builtin/packages/expat/package.py
+++ b/var/spack/repos/builtin/packages/expat/package.py
@@ -7,6 +7,7 @@ class Expat(Package):
 
     version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd')
 
+    depends_on('cmake')
 
     def install(self, spec, prefix):
 
diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py
index 4d2b964242..bc129aaf1a 100644
--- a/var/spack/repos/builtin/packages/fftw/package.py
+++ b/var/spack/repos/builtin/packages/fftw/package.py
@@ -47,6 +47,8 @@ class Fftw(Package):
 
     depends_on('mpi', when='+mpi')
 
+    # TODO : add support for architecture specific optimizations as soon as targets are supported
+
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix,
                    '--enable-shared',
diff --git a/var/spack/repos/builtin/packages/fish/package.py b/var/spack/repos/builtin/packages/fish/package.py
index 1225558705..b5a4a2d209 100644
--- a/var/spack/repos/builtin/packages/fish/package.py
+++ b/var/spack/repos/builtin/packages/fish/package.py
@@ -7,7 +7,8 @@ class Fish(Package):
 
     homepage = "http://fishshell.com/"
     url      = "http://fishshell.com/files/2.2.0/fish-2.2.0.tar.gz"
-    list_url = homepage
+    list_url = "http://fishshell.com/files/"
+    list_depth = 2
 
     version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a')
 
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 3e5895cfb8..f8958ee290 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -36,8 +36,6 @@ class Gcc(Package):
     list_url = 'http://open-source-box.org/gcc/'
     list_depth = 2
 
-    DEPENDS_ON_ISL_PREDICATE = '@5.0:'
-
     version('5.3.0', 'c9616fd448f980259c31de613e575719')
     version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467')
     version('4.9.3', '6f831b4d251872736e8e9cc09746f327')
@@ -53,12 +51,11 @@ class Gcc(Package):
 
     depends_on("mpfr")
     depends_on("gmp")
-    depends_on("mpc")     # when @4.5:
+    depends_on("mpc", when='@4.5:')
+    depends_on("isl", when='@5.0:')
     depends_on("binutils~libiberty", when='~gold')
     depends_on("binutils~libiberty+gold", when='+gold')
 
-    # Save these until we can do optional deps.
-    depends_on("isl", when=DEPENDS_ON_ISL_PREDICATE)
     #depends_on("ppl")
     #depends_on("cloog")
 
@@ -91,7 +88,7 @@ class Gcc(Package):
                             "--with-as=%s/bin/as" % spec['binutils'].prefix]
         options.extend(binutils_options)
         # Isl
-        if spec.satisfies(Gcc.DEPENDS_ON_ISL_PREDICATE):
+        if 'isl' in spec:
             isl_options = ["--with-isl=%s" % spec['isl'].prefix]
             options.extend(isl_options)
 
diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py
index dd02b426b9..b346fe80c2 100644
--- a/var/spack/repos/builtin/packages/gdb/package.py
+++ b/var/spack/repos/builtin/packages/gdb/package.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py
new file mode 100644
index 0000000000..5fe8399308
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gromacs/package.py
@@ -0,0 +1,56 @@
+from spack import *
+
+
+class Gromacs(Package):
+    """
+    GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for
+    simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry
+    department of University of Groningen, and is now maintained by contributors in universities and research centers
+    across the world.
+
+    GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs.
+    It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is
+    released under the GNU Lesser General Public License.
+    """
+
+    homepage = 'http://www.gromacs.org'
+    url = 'ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.2.tar.gz'
+
+    version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98')
+
+    variant('mpi', default=True, description='Activate MPI support')
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('debug', default=False, description='Enables debug mode')
+    variant('double', default=False, description='Produces a double precision version of the executables')
+
+    depends_on('mpi', when='+mpi')
+
+    depends_on('fftw')
+
+    # TODO : add GPU support
+
+    def install(self, spec, prefix):
+
+        options = []
+
+        if '+mpi' in spec:
+            options.append('-DGMX_MPI:BOOL=ON')
+
+        if '+double' in spec:
+            options.append('-DGMX_DOUBLE:BOOL=ON')
+
+        if '~shared' in spec:
+            options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
+
+        if '+debug' in spec:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
+        else:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Release')
+
+        options.extend(std_cmake_args)
+
+        with working_dir('spack-build', create=True):
+
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py
new file mode 100644
index 0000000000..ac6435f2a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hdf/package.py
@@ -0,0 +1,45 @@
+from spack import *
+
+class Hdf(Package):
+    """HDF4 (also known as HDF) is a library and multi-object
+    file format for storing and managing data between machines."""
+
+    homepage = "https://www.hdfgroup.org/products/hdf4/"
+    url      = "https://www.hdfgroup.org/ftp/HDF/releases/HDF4.2.11/src/hdf-4.2.11.tar.gz"
+    list_url = "https://www.hdfgroup.org/ftp/HDF/releases/"
+    list_depth = 3
+
+    version('4.2.11', '063f9928f3a19cc21367b71c3b8bbf19')
+
+    variant('szip', default=False, description="Enable szip support")
+
+    depends_on("jpeg")
+    depends_on("szip", when='+szip')
+    depends_on("zlib")
+
+
+    def url_for_version(self, version):
+       return "https://www.hdfgroup.org/ftp/HDF/releases/HDF" + str(version) + "/src/hdf-" + str(version) + ".tar.gz"
+
+
+    def install(self, spec, prefix):
+        config_args = [
+            'CFLAGS=-fPIC',
+            '--prefix=%s' % prefix,
+            '--with-jpeg=%s' % spec['jpeg'].prefix,
+            '--with-zlib=%s' % spec['zlib'].prefix,
+            '--disable-netcdf',  # must be disabled to build NetCDF with HDF4 support
+            '--enable-fortran',
+            '--disable-shared',  # fortran and shared libraries are not compatible
+            '--enable-static',
+            '--enable-production'
+        ]
+
+        # SZip support
+        if '+szip' in spec:
+            config_args.append('--with-szlib=%s' % spec['szip'].prefix)
+
+        configure(*config_args)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index ac78d8e961..ed4e7c35c9 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -42,15 +42,18 @@ class Hdf5(Package):
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
 
     variant('debug', default=False, description='Builds a debug version of the library')
+    variant('shared', default=True, description='Builds a shared version of the library')
 
     variant('cxx', default=True, description='Enable C++ support')
     variant('fortran', default=True, description='Enable Fortran support')
-    variant('unsupported', default=False, description='Enables unsupported configuration options')
+    variant('unsupported', default=True, description='Enables unsupported configuration options')
 
     variant('mpi', default=False, description='Enable MPI support')
+    variant('szip', default=False, description='Enable szip support')
     variant('threadsafe', default=False, description='Enable thread-safe capabilities')
 
     depends_on("mpi", when='+mpi')
+    depends_on("szip", when='+szip')
     depends_on("zlib")
 
     def validate(self, spec):
@@ -76,6 +79,11 @@ class Hdf5(Package):
         else:
             extra_args.append('--enable-production')
 
+        if '+shared' in spec:
+            extra_args.append('--enable-shared')
+        else:
+            extra_args.append('--enable-static-exec')
+
         if '+unsupported' in spec:
             extra_args.append("--enable-unsupported")
 
@@ -105,6 +113,9 @@ class Hdf5(Package):
             if '+fortran' in spec:
                 extra_args.append("FC=%s" % spec['mpi'].prefix.bin + "/mpifort")
 
+        if '+szip' in spec:
+            extra_args.append("--with-szlib=%s" % spec['szip'].prefix)
+
         if '+threadsafe' in spec:
             extra_args.extend([
                 '--enable-threadsafe',
@@ -114,7 +125,6 @@ class Hdf5(Package):
         configure(
             "--prefix=%s" % prefix,
             "--with-zlib=%s" % spec['zlib'].prefix,
-            "--enable-shared",  # TODO : this should be enabled by default, remove it?
             *extra_args)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py
new file mode 100644
index 0000000000..3dae3c4170
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpx5/package.py
@@ -0,0 +1,52 @@
+from spack import *
+import os
+
+class Hpx5(Package):
+    """The HPX-5 Runtime System. HPX-5 (High Performance ParalleX) is an
+    open source, portable, performance-oriented runtime developed at
+    CREST (Indiana University). HPX-5 provides a distributed
+    programming model allowing programs to run unmodified on systems
+    from a single SMP to large clusters and supercomputers with
+    thousands of nodes. HPX-5 supports a wide variety of Intel and ARM
+    platforms. It is being used by a broad range of scientific
+    applications enabling scientists to write code that performs and
+    scales better than contemporary runtimes."""
+    homepage = "http://hpx.crest.iu.edu"
+    url      = "http://hpx.crest.iu.edu/release/hpx-2.0.0.tar.gz"
+
+    version('2.0.0', '3d2ff3aab6c46481f9ec65c5b2bfe7a6')
+    version('1.3.0', '2260ecc7f850e71a4d365a43017d8cee')
+    version('1.2.0', '4972005f85566af4afe8b71afbf1480f')
+    version('1.1.0', '646afb460ecb7e0eea713a634933ce4f')
+    version('1.0.0', '8020822adf6090bd59ed7fe465f6c6cb')
+
+    variant('debug', default=False, description='Build a debug version of HPX-5')
+    variant('photon', default=False, description='Enable Photon support')
+    variant('mpi', default=False, description='Enable MPI support')
+
+    depends_on("mpi", when='+mpi')
+    depends_on("mpi", when='+photon')
+
+    def install(self, spec, prefix):
+        extra_args = []
+        if '+debug' in spec:
+            extra_args.extend([
+                '--enable-debug',
+                'CFLAGS=-g -O0'
+            ])
+        else:
+            extra_args.append('CFLAGS=-O3')
+
+        if '+mpi' in spec:
+            extra_args.append('--enable-mpi')
+
+        if '+photon' in spec:
+            extra_args.extend([
+                '--enable-mpi',
+                '--enable-photon'
+            ])
+
+        os.chdir("./hpx/")
+        configure('--prefix=%s' % prefix, *extra_args)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index 7ebede76a3..ab7205646e 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -14,15 +14,18 @@ class Hwloc(Package):
        efficiently."""
     homepage = "http://www.open-mpi.org/projects/hwloc/"
     url      = "http://www.open-mpi.org/software/hwloc/v1.9/downloads/hwloc-1.9.tar.gz"
+    list_url = "http://www.open-mpi.org/software/hwloc/"
+    list_depth = 3
 
-    version('1.11.2', '486169cbe111cdea57be12638828ebbf',
-            url='http://www.open-mpi.org/software/hwloc/v1.11/downloads/hwloc-1.11.2.tar.bz2')
-    version('1.11.1', '002742efd3a8431f98d6315365a2b543',
-            url='http://www.open-mpi.org/software/hwloc/v1.11/downloads/hwloc-1.11.1.tar.bz2')
-    version('1.9', '1f9f9155682fe8946a97c08896109508')
+    version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23')
+    version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc')
+    version('1.9',    '1f9f9155682fe8946a97c08896109508')
 
     depends_on('libpciaccess')
 
+    def url_for_version(self, version):
+        return "http://www.open-mpi.org/software/hwloc/v%s/downloads/hwloc-%s.tar.gz" % (version.up_to(2), version)
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 0f7f14dd89..242ee100d7 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import os
 
 class Hypre(Package):
     """Hypre is a library of high performance preconditioners that
@@ -8,8 +9,11 @@ class Hypre(Package):
     homepage = "http://computation.llnl.gov/project/linear_solvers/software.php"
     url      = "http://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz"
 
+    version('2.10.1', 'dc048c4cabb3cd549af72591474ad674')
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
 
+    variant('shared', default=True, description="Build shared library version (disables static library)")
+
     depends_on("mpi")
     depends_on("blas")
     depends_on("lapack")
@@ -17,16 +21,26 @@ class Hypre(Package):
     def install(self, spec, prefix):
         blas_dir = spec['blas'].prefix
         lapack_dir = spec['lapack'].prefix
+        mpi_dir = spec['mpi'].prefix
+
+        os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc')
+        os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx')
+        os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77')
+
+
+        configure_args = [
+                "--prefix=%s" % prefix,
+                "--with-lapack-libs=lapack",
+                "--with-lapack-lib-dirs=%s/lib" % lapack_dir,
+                "--with-blas-libs=blas",
+                "--with-blas-lib-dirs=%s/lib" % blas_dir]
+        if '+shared' in self.spec:
+            configure_args.append("--enable-shared")
 
         # Hypre's source is staged under ./src so we'll have to manually
         # cd into it.
         with working_dir("src"):
-            configure(
-                "--prefix=%s" % prefix,
-                "--with-blas-libs=blas",
-                "--with-blas-lib-dirs=%s/lib" % blas_dir,
-                "--with-lapack-libs=\"lapack blas\"",
-                "--with-lapack-lib-dirs=%s/lib" % lapack_dir,
-                "--with-MPI")
+            configure(*configure_args)
+
             make()
             make("install")
diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index f8f5fc21bd..cbcc53ac0a 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -28,7 +28,7 @@ class Jdk(Package):
         '-H', # specify required License Agreement cookie
         'Cookie: oraclelicense=accept-securebackup-cookie']
 
-    def do_fetch(self):
+    def do_fetch(self, mirror_only=False):
         # Add our custom curl commandline options
         tty.msg(
             "[Jdk] Adding required commandline options to curl " +
@@ -39,7 +39,7 @@ class Jdk(Package):
             spack.curl.add_default_arg(option)
 
         # Now perform the actual fetch
-        super(Jdk, self).do_fetch()
+        super(Jdk, self).do_fetch(mirror_only)
 
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py
index bcd5212b9e..faed8bad37 100644
--- a/var/spack/repos/builtin/packages/libedit/package.py
+++ b/var/spack/repos/builtin/packages/libedit/package.py
@@ -7,6 +7,8 @@ class Libedit(Package):
 
     version('3.1', '43cdb5df3061d78b5e9d59109871b4f6', url="http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz")
 
+    depends_on('ncurses')
+
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
 
diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py
index 11b1083d67..714a155dc0 100644
--- a/var/spack/repos/builtin/packages/libevent/package.py
+++ b/var/spack/repos/builtin/packages/libevent/package.py
@@ -22,9 +22,16 @@ class Libevent(Package):
     version('2.0.13', 'af786b4b3f790c9d3279792edf7867fc')
     version('2.0.12', '42986228baf95e325778ed328a93e070')
 
+    variant('openssl', default=True, description="Build with encryption enabled at the libevent level.")
+    depends_on('openssl', when='+openssl')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure_args = []
+        if '+openssl' in spec:
+            configure_args.append('--enable-openssl')
+        else:
+            configure_args.append('--enable-openssl')
 
+        configure("--prefix=%s" % prefix, *configure_args)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/libgpg-error/package.py b/var/spack/repos/builtin/packages/libgpg-error/package.py
index 6c1d1a10a7..dd5fc2408a 100644
--- a/var/spack/repos/builtin/packages/libgpg-error/package.py
+++ b/var/spack/repos/builtin/packages/libgpg-error/package.py
@@ -9,6 +9,7 @@ class LibgpgError(Package):
     homepage = "https://www.gnupg.org/related_software/libgpg-error"
     url      = "ftp://ftp.gnupg.org/gcrypt/libgpg-error/libgpg-error-1.18.tar.bz2"
 
+    version('1.21', 'ab0b5aba6d0a185b41d07bda804fd8b2')
     version('1.18', '12312802d2065774b787cbfc22cc04e9')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py
new file mode 100644
index 0000000000..4b486198ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libsigsegv/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class Libsigsegv(Package):
+    """GNU libsigsegv is a library for handling page faults in user mode."""
+    homepage = "https://www.gnu.org/software/libsigsegv/"
+    url      = "ftp://ftp.gnu.org/gnu/libsigsegv/libsigsegv-2.10.tar.gz"
+
+    version('2.10', '7f96fb1f65b3b8cbc1582fb7be774f0f')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--enable-shared')
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index a2b2c6eccc..280e400f69 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -1,5 +1,5 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
@@ -34,7 +34,7 @@ class Llvm(Package):
        it is the full name of the project.
     """
     homepage = 'http://llvm.org/'
-    url = 'http://llvm.org/releases/3.7.0/llvm-3.7.0.src.tar.xz'
+    url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz'
 
     version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # currently required by mesa package
 
@@ -118,6 +118,36 @@ class Llvm(Package):
                 }
     releases = [
                   {
+                    'version' : 'trunk',
+                    'repo' : 'http://llvm.org/svn/llvm-project/llvm/trunk',
+                    'resources' : {
+                        'compiler-rt' : 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
+                        'openmp' : 'http://llvm.org/svn/llvm-project/openmp/trunk',
+                        'polly' : 'http://llvm.org/svn/llvm-project/polly/trunk',
+                        'libcxx' : 'http://llvm.org/svn/llvm-project/libcxx/trunk',
+                        'libcxxabi' : 'http://llvm.org/svn/llvm-project/libcxxabi/trunk',
+                        'clang' : 'http://llvm.org/svn/llvm-project/cfe/trunk',
+                        'clang-tools-extra' : 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
+                        'lldb' : 'http://llvm.org/svn/llvm-project/lldb/trunk',
+                        'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
+                        }
+                  },
+                  {
+                    'version' : '3.7.1',
+                    'md5':'bf8b3a2c79e61212c5409041dfdbd319',
+                    'resources' : {
+                        'compiler-rt' : '1c6975daf30bb3b0473b53c3a1a6ff01',
+                        'openmp' : 'b4ad08cda4e5c22e42b66062b140438e',
+                        'polly' : '3a2a7367002740881637f4d47bca4dc3',
+                        'libcxx' : 'f9c43fa552a10e14ff53b94d04bea140',
+                        'libcxxabi' : '52d925afac9f97e9dcac90745255c169',
+                        'clang' : '0acd026b5529164197563d135a8fd83e',
+                        'clang-tools-extra' : '5d49ff745037f061a7c86aeb6a24c3d2',
+                        'lldb' : 'a106d8a0d21fc84d76953822fbaf3398',
+                        'llvm-libunwind' : '814bd52c9247c5d04629658fbcb3ab8c',
+                        }
+                  },
+                  {
                     'version' : '3.7.0',
                     'md5':'b98b9495e5655a672d6cb83e1a180f8e',
                     'resources' : {
@@ -161,15 +191,25 @@ class Llvm(Package):
                ]
 
     for release in releases:
-        version(release['version'], release['md5'], url=llvm_url % release)
-
-        for name, md5 in release['resources'].items():
-            resource(name=name,
-                     url=resources[name]['url'] % release,
-                     md5=md5,
-                     destination=resources[name]['destination'],
-                     when='@%(version)s' % release,
-                     placement=resources[name].get('placement', None))
+        if release['version'] == 'trunk' :
+            version(release['version'], svn=release['repo'])
+
+            for name, repo in release['resources'].items():
+                resource(name=name,
+                         svn=repo,
+                         destination=resources[name]['destination'],
+                         when='@%(version)s' % release,
+                         placement=resources[name].get('placement', None))
+        else:
+            version(release['version'], release['md5'], url=llvm_url % release)
+
+            for name, md5 in release['resources'].items():
+                resource(name=name,
+                         url=resources[name]['url'] % release,
+                         md5=md5,
+                         destination=resources[name]['destination'],
+                         when='@%(version)s' % release,
+                         placement=resources[name].get('placement', None))
 
     def install(self, spec, prefix):
         env['CXXFLAGS'] = self.compiler.cxx11_flag
diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
new file mode 100644
index 0000000000..a4b9dcb623
--- /dev/null
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -0,0 +1,25 @@
+from spack import *
+
+class M4(Package):
+    """GNU M4 is an implementation of the traditional Unix macro processor."""
+    homepage = "https://www.gnu.org/software/m4/m4.html"
+    url      = "ftp://ftp.gnu.org/gnu/m4/m4-1.4.17.tar.gz"
+
+    version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76')
+
+    patch('pgi.patch', when='@1.4.17')
+
+    variant('sigsegv', default=True, description="Build the libsigsegv dependency")
+
+    depends_on('libsigsegv', when='+sigsegv')
+
+    def install(self, spec, prefix):
+        configure_args = []
+        if 'libsigsegv' in spec:
+            configure_args.append('--with-libsigsegv-prefix=%s' % spec['libsigsegv'].prefix)
+        else:
+            configure_args.append('--without-libsigsegv-prefix')
+
+        configure("--prefix=%s" % prefix, *configure_args)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/m4/pgi.patch b/var/spack/repos/builtin/packages/m4/pgi.patch
new file mode 100644
index 0000000000..1ad63e2cf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/m4/pgi.patch
@@ -0,0 +1,10 @@
+--- a/lib/config.hin
++++ b/lib/config.hin
+@@ -1510,6 +1510,7 @@
+       ? defined __GNUC_STDC_INLINE__ && __GNUC_STDC_INLINE__ \
+       : (199901L <= __STDC_VERSION__ \
+          && !defined __HP_cc \
++         && !defined __PGI \
+          && !(defined __SUNPRO_C && __STDC__))) \
+      && !defined _GL_EXTERN_INLINE_APPLE_BUG)
+ # define _GL_INLINE inline
diff --git a/var/spack/repos/builtin/packages/mpc/package.py b/var/spack/repos/builtin/packages/mpc/package.py
index 50477a0ccb..108fec678f 100644
--- a/var/spack/repos/builtin/packages/mpc/package.py
+++ b/var/spack/repos/builtin/packages/mpc/package.py
@@ -37,6 +37,12 @@ class Mpc(Package):
     depends_on("gmp")
     depends_on("mpfr")
 
+    def url_for_version(self, version):
+        if version < Version("1.0.1"):
+            return "http://www.multiprecision.org/mpc/download/mpc-%s.tar.gz" % version
+        else:
+            return "ftp://ftp.gnu.org/gnu/mpc/mpc-%s.tar.gz" % version
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 405e223b5a..e2b3654c19 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -48,10 +48,11 @@ class Mpich(Package):
 
     def setup_dependent_environment(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
-        os.environ['MPICH_CC']  = 'cc'
-        os.environ['MPICH_CXX'] = 'c++'
-        os.environ['MPICH_F77'] = 'f77'
-        os.environ['MPICH_F90'] = 'f90'
+        os.environ['MPICH_CC']  = os.environ['CC']
+        os.environ['MPICH_CXX'] = os.environ['CXX']
+        os.environ['MPICH_F77'] = os.environ['F77']
+        os.environ['MPICH_F90'] = os.environ['FC']
+        os.environ['MPICH_FC'] = os.environ['FC']
 
         module.mpicc = join_path(self.prefix.bin, 'mpicc')
 
diff --git a/var/spack/repos/builtin/packages/ndiff/package.py b/var/spack/repos/builtin/packages/ndiff/package.py
new file mode 100644
index 0000000000..10e445c81e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ndiff/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+class Ndiff(Package):
+    """The ndiff tool is a binary utility that compares putatively similar files
+       while ignoring small numeric differernces. This utility is most often used
+       to compare files containing a lot of floating-point numeric data that
+       may be slightly different due to numeric error."""
+
+    homepage = "http://ftp.math.utah.edu/pub/ndiff/"
+    url      = "http://ftp.math.utah.edu/pub/ndiff/ndiff-2.00.tar.gz"
+
+    version('2.00', '885548b4dc26e72c5455bebb5ba6c16d')
+    version('1.00', 'f41ffe5d12f36cd36b6311acf46eccdc')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        mkdirp(prefix.bin)
+        mkdirp('%s/lib' % prefix.share)
+
+        make('install-exe', 'install-shrlib')
diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
new file mode 100644
index 0000000000..b83e964b00
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class NetcdfCxx4(Package):
+    """C++ interface for NetCDF4"""
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
+    url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.2.tar.gz"
+
+    version('4.2', 'd019853802092cf686254aaba165fc81')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
new file mode 100644
index 0000000000..e4e33445e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class NetcdfFortran(Package):
+    """Fortran interface for NetCDF4"""
+
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
+    url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz"
+
+    version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/netcdf/netcdf-4.3.3-mpi.patch b/var/spack/repos/builtin/packages/netcdf/netcdf-4.3.3-mpi.patch
deleted file mode 100644
index 46dda5fc9d..0000000000
--- a/var/spack/repos/builtin/packages/netcdf/netcdf-4.3.3-mpi.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff -Nur netcdf-4.3.3/CMakeLists.txt netcdf-4.3.3.mpi/CMakeLists.txt
---- netcdf-4.3.3/CMakeLists.txt	2015-02-12 16:44:35.000000000 -0500
-+++ netcdf-4.3.3.mpi/CMakeLists.txt	2015-10-14 16:44:41.176300658 -0400
-@@ -753,6 +753,7 @@
-     SET(USE_PARALLEL OFF CACHE BOOL "")
-     MESSAGE(STATUS "Cannot find HDF5 library built with parallel support. Disabling parallel build.")
-   ELSE()
-+    FIND_PACKAGE(MPI REQUIRED)
-     SET(USE_PARALLEL ON CACHE BOOL "")
-     SET(STATUS_PARALLEL "ON")
-   ENDIF()
-diff -Nur netcdf-4.3.3/liblib/CMakeLists.txt netcdf-4.3.3.mpi/liblib/CMakeLists.txt
---- netcdf-4.3.3/liblib/CMakeLists.txt	2015-02-12 16:44:35.000000000 -0500
-+++ netcdf-4.3.3.mpi/liblib/CMakeLists.txt	2015-10-14 16:44:57.757793634 -0400
-@@ -71,6 +71,10 @@
-   SET(TLL_LIBS ${TLL_LIBS} ${CURL_LIBRARY})
- ENDIF()
- 
-+IF(USE_PARALLEL)
-+  SET(TLL_LIBS ${TLL_LIBS} ${MPI_C_LIBRARIES})
-+ENDIF()
-+
- IF(USE_HDF4)
-   SET(TLL_LIBS ${TLL_LIBS} ${HDF4_LIBRARIES})
- ENDIF()
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index 239644d894..227362399a 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -1,28 +1,76 @@
 from spack import *
 
+
 class Netcdf(Package):
     """NetCDF is a set of software libraries and self-describing, machine-independent
-        data formats that support the creation, access, and sharing of array-oriented
-        scientific data."""
+    data formats that support the creation, access, and sharing of array-oriented
+    scientific data."""
 
-    homepage = "http://www.unidata.ucar.edu/software/netcdf/"
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz"
 
+    version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
     version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
 
-    patch('netcdf-4.3.3-mpi.patch')
+    variant('mpi', default=True, description='Enables MPI parallelism')
+    variant('hdf4',    default=False, description="Enable HDF4 support")
 
     # Dependencies:
-    depends_on("cmake @2.8.12:")
-        # >HDF5
-    depends_on("hdf5")
+    depends_on("curl")  # required for DAP support
+    depends_on("hdf", when='+hdf4')
+    depends_on("hdf5+mpi~cxx", when='+mpi')  # required for NetCDF-4 support
+    depends_on("hdf5~mpi", when='~mpi')  # required for NetCDF-4 support
+    depends_on("zlib")  # required for NetCDF-4 support
 
     def install(self, spec, prefix):
-        with working_dir('spack-build', create=True):
-            cmake('..',
-                "-DCMAKE_INSTALL_PREFIX:PATH=%s" % prefix,
-                "-DENABLE_DAP:BOOL=OFF", # Disable DAP.
-                "-DBUILD_SHARED_LIBS:BOOL=OFF") # Don't build shared libraries (use static libs).
-
-            make()
-            make("install")
+        # Environment variables
+        CPPFLAGS = []
+        LDFLAGS  = []
+        LIBS     = []
+
+        config_args = [
+            "--prefix=%s" % prefix,
+            "--enable-fsync",
+            "--enable-v2",
+            "--enable-utilities",
+            "--enable-shared",
+            "--enable-static",
+            "--enable-largefile",
+            # necessary for HDF5 support
+            "--enable-netcdf-4",
+            "--enable-dynamic-loading",
+            # necessary for DAP support
+            "--enable-dap"
+        ]
+
+        if '+mpi' in spec:
+            config_args.append('--enable-parallel4')
+
+        CPPFLAGS.append("-I%s/include" % spec['hdf5'].prefix)
+        LDFLAGS.append( "-L%s/lib"     % spec['hdf5'].prefix)
+
+        # HDF4 support
+        # As of NetCDF 4.1.3, "--with-hdf4=..." is no longer a valid option
+        # You must use the environment variables CPPFLAGS and LDFLAGS
+        if '+hdf4' in spec:
+            config_args.append("--enable-hdf4")
+            CPPFLAGS.append("-I%s/include" % spec['hdf'].prefix)
+            LDFLAGS.append( "-L%s/lib"     % spec['hdf'].prefix)
+            LIBS.append(    "-l%s"         % "jpeg")
+
+        if 'szip' in spec:
+            CPPFLAGS.append("-I%s/include" % spec['szip'].prefix)
+            LDFLAGS.append( "-L%s/lib"     % spec['szip'].prefix)
+            LIBS.append(    "-l%s"         % "sz")
+
+        # Fortran support
+        # In version 4.2+, NetCDF-C and NetCDF-Fortran have split.
+        # Use the netcdf-fortran package to install Fortran support.
+
+        config_args.append('CPPFLAGS=%s' % ' '.join(CPPFLAGS))
+        config_args.append('LDFLAGS=%s'  % ' '.join(LDFLAGS))
+        config_args.append('LIBS=%s'     % ' '.join(LIBS))
+
+        configure(*config_args)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 5be91c4a40..22d538560e 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -22,8 +22,8 @@ class NetlibScalapack(Package):
     
     def install(self, spec, prefix):       
         options = [
-            "-DBUILD_SHARED_LIBS:BOOL=%s" % 'ON' if '+shared' in spec else 'OFF',
-            "-DBUILD_STATIC_LIBS:BOOL=%s" % 'OFF' if '+shared' in spec else 'ON',
+            "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'),
+            "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'),
             "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", # forces scalapack to use find_package(LAPACK)
             ]
 
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 9c8fa1c694..3c909360a4 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -19,7 +19,9 @@ class Openblas(Package):
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'blas.a')
             symlink('libopenblas.a', 'libblas.a')
+            symlink('libopenblas.so', 'libblas.so')
 
         # Lapack virtual package should provide liblapack.a
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'liblapack.a')
+            symlink('libopenblas.so', 'liblapack.so')
diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py
new file mode 100644
index 0000000000..99b555323f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencv/package.py
@@ -0,0 +1,50 @@
+from spack import *
+
+
+class Opencv(Package):
+    """
+    OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C++, C,
+    Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for
+    computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library
+    can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware
+    acceleration of the underlying heterogeneous compute platform. Adopted all around the world, OpenCV has more than
+    47 thousand people of user community and estimated number of downloads exceeding 9 million. Usage ranges from
+    interactive art, to mines inspection, stitching maps on the web or through advanced robotics.
+    """
+    homepage = 'http://opencv.org/'
+    url = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz'
+
+    version('3.1.0', '70e1dd07f0aa06606f1bc0e3fa15abd3')
+
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('debug', default=False, description='Builds a debug version of the libraries')
+
+    variant('eigen', default=True, description='Activates support for eigen')
+    variant('ipp', default=True, description='Activates support for IPP')
+
+    depends_on('zlib')
+    depends_on('libpng')
+    depends_on('libjpeg-turbo')
+    depends_on('libtiff')
+
+    depends_on('python')
+    depends_on('py-numpy')
+
+    depends_on('eigen', when='+eigen')
+
+    # FIXME : GUI extensions missing
+    # FIXME : CUDA extensions still missing
+
+    def install(self, spec, prefix):
+        cmake_options = []
+        cmake_options.extend(std_cmake_args)
+
+        cmake_options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                              '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
+                              '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF',
+                              '-DWITH_IPP:BOOL=%s' % ('ON' if '+ipp' in spec else 'OFF')])
+
+        with working_dir('spack_build', create=True):
+            cmake('..', *cmake_options)
+            make('VERBOSE=1')
+            make("install")
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index bbb169ec6b..70afaf4038 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -1,3 +1,6 @@
+import urllib
+import llnl.util.tty as tty
+
 from spack import *
 
 class Openssl(Package):
@@ -10,12 +13,51 @@ class Openssl(Package):
     url      = "http://www.openssl.org/source/openssl-1.0.1h.tar.gz"
 
     version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
+    version('1.0.1r', '1abd905e079542ccae948af37e393d28')
     version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
     version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
+    version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
+    version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
 
     depends_on("zlib")
     parallel = False
 
+    def url_for_version(self, version):
+        # This URL is computed pinging the place where the latest version is stored. To avoid slowdown
+        # due to repeated pinging, we store the URL in a private class attribute to do the job only once per version
+        openssl_urls = getattr(Openssl, '_openssl_url', {})
+        openssl_url = openssl_urls.get(version, None)
+        # Same idea, but just to avoid issuing the same message multiple times
+        warnings_given_to_user = getattr(Openssl, '_warnings_given', {})
+        if openssl_url is None:
+            latest = 'http://www.openssl.org/source/openssl-{version}.tar.gz'
+            older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz'
+            # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then
+            # return the url for older format
+            version_number = '.'.join([str(x) for x in version[:-1]])
+            older_url = older.format(version_number=version_number, version_full=version)
+            latest_url = latest.format(version=version)
+            response = urllib.urlopen(latest.format(version=version))
+            if response.getcode() == 404:
+                openssl_url = older_url
+                # Checks if we already warned the user for this particular version of OpenSSL.
+                # If not we display a warning message and mark this version
+                if not warnings_given_to_user.get(version, False):
+                    tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ')
+                    tty.warn('Consider updating to the latest version of this package.')
+                    tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
+                    warnings_given_to_user[version] = True
+            else:
+                openssl_url = latest_url
+            # Store the computed URL
+            openssl_urls[version] = openssl_url
+            # Store the updated dictionary of URLS
+            Openssl._openssl_url = openssl_urls
+            # Store the updated dictionary of warnings
+            Openssl._warnings_given = warnings_given_to_user
+
+        return openssl_url
+
     def install(self, spec, prefix):
         # OpenSSL uses a variable APPS in its Makefile. If it happens to be set
         # in the environment, then this will override what is set in the
diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py
index df43625bf5..79dad3a3d2 100644
--- a/var/spack/repos/builtin/packages/pango/package.py
+++ b/var/spack/repos/builtin/packages/pango/package.py
@@ -16,4 +16,4 @@ class Pango(Package):
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
-        make("install")
+        make("install", parallel=False)
diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
new file mode 100644
index 0000000000..62a8f7ca0b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -0,0 +1,20 @@
+from spack import *
+
+class ParallelNetcdf(Package):
+    """Parallel netCDF (PnetCDF) is a library providing high-performance
+    parallel I/O while still maintaining file-format compatibility with
+    Unidata's NetCDF."""
+
+    homepage = "https://trac.mcs.anl.gov/projects/parallel-netcdf"
+    url      = "http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/parallel-netcdf-1.6.1.tar.gz"
+
+    version('1.6.1', '62a094eb952f9d1e15f07d56e535052604f1ac34')
+
+    depends_on("m4")
+    depends_on("mpi")
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix,
+                  "--with-mpi=%s" % spec['mpi'].prefix)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index aaab352e66..ccf2d14c06 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -2,9 +2,11 @@ from spack import *
 
 class Paraview(Package):
     homepage = 'http://www.paraview.org'
-    url      = 'http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz'
+    url      = 'http://www.paraview.org/files/v5.0/ParaView-v'
+    _url_str = 'http://www.paraview.org/files/v%s/ParaView-v%s-source.tar.gz'
 
-    version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378', url='http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz')
+    version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378')
+    version('5.0.0', '4598f0b421460c8bbc635c9a1c3bdbee')
 
     variant('python', default=False, description='Enable Python support')
 
@@ -14,6 +16,7 @@ class Paraview(Package):
 
     variant('osmesa', default=False, description='Enable OSMesa support')
     variant('qt', default=False, description='Enable Qt support')
+    variant('opengl2', default=False, description='Enable OPengl2 backend')
 
     depends_on('python', when='+python')
     depends_on('py-numpy', when='+python')
@@ -24,8 +27,8 @@ class Paraview(Package):
 
     depends_on('bzip2')
     depends_on('freetype')
-    depends_on('hdf5')
     depends_on('hdf5+mpi', when='+mpi')
+    depends_on('hdf5~mpi', when='~mpi')
     depends_on('jpeg')
     depends_on('libpng')
     depends_on('libtiff')
@@ -34,6 +37,11 @@ class Paraview(Package):
     #depends_on('protobuf') # version mismatches?
     #depends_on('sqlite') # external version not supported
     depends_on('zlib')
+    
+    def url_for_version(self, version):
+        """Handle ParaView version-based custom URLs."""
+        return self._url_str % (version.up_to(2), version)
+    
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 87f700629d..5be187f348 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -1,40 +1,86 @@
+import os
 from spack import *
 
+
 class Petsc(Package):
-    """PETSc is a suite of data structures and routines for the
-       scalable (parallel) solution of scientific applications modeled by
-       partial differential equations."""
+    """
+    PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications
+    modeled by partial differential equations.
+    """
 
     homepage = "http://www.mcs.anl.gov/petsc/index.html"
-    url      = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
+    url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
 
+    version('3.6.3', '91dd3522de5a5ef039ff8f50800db606')
     version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f')
     version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13')
     version('3.5.1', 'a557e029711ebf425544e117ffa44d8f')
 
-    depends_on("python @2.6:2.9")   # requires Python for building
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('mpi', default=True, description='Activates MPI support')
+    variant('double', default=True, description='Switches between single and double precision')
+
+    variant('metis', default=True, description='Activates support for metis and parmetis')
+    variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)')
+    variant('boost', default=True, description='Activates support for Boost')
+    variant('hypre', default=True, description='Activates support for Hypre')
+
+    # Build dependencies
+    depends_on('python @2.6:2.9')  # requires Python for building
+
+    # Virtual dependencies
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('mpi', when='+mpi')
 
-    depends_on("boost")
-    depends_on("blas")
-    depends_on("lapack")
-    depends_on("hypre")
-    depends_on("parmetis")
-    depends_on("metis")
-    depends_on("hdf5+mpi")
-    depends_on("mpi")
+    # Other dependencies
+    depends_on('boost', when='+boost')
+    depends_on('metis', when='+metis')
+
+    depends_on('hdf5~cxx~unsupported+mpi', when='+hdf5+mpi')
+    depends_on('parmetis', when='+metis+mpi')
+    depends_on('hypre', when='+hypre+mpi')
+
+    def mpi_dependent_options(self):
+        if '~mpi' in self.spec:
+            compiler_opts = [
+                '--with-cc=%s' % os.environ['CC'],
+                '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'),
+                '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'),
+                '--with-mpi=0'
+            ]
+            error_message_fmt = '\t{library} support requires "+mpi" to be activated'
+            errors = [error_message_fmt.format(library=x) for x in ('hdf5', 'hypre') if ('+'+x) in self.spec]
+            if errors:
+                errors = ['incompatible variants given'] + errors
+                raise RuntimeError('\n'.join(errors))
+        else:
+            compiler_opts = [
+                '--with-mpi=1',
+                '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
+            ]
+        return compiler_opts
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
-                  "--with-blas-lib=%s/libblas.a"     % spec['blas'].prefix.lib,
-                  "--with-lapack-lib=%s/liblapack.a" % spec['lapack'].prefix.lib,
-                  "--with-boost-dir=%s"              % spec['boost'].prefix,
-                  "--with-hypre-dir=%s"              % spec['hypre'].prefix,
-                  "--with-parmetis-dir=%s"           % spec['parmetis'].prefix,
-                  "--with-metis-dir=%s"              % spec['metis'].prefix,
-                  "--with-hdf5-dir=%s"               % spec['hdf5'].prefix,
-                  "--with-mpi-dir=%s"                % spec['mpi'].prefix,
-                  "--with-shared-libraries=0")
+        options = []
+        options.extend(self.mpi_dependent_options())
+        options.extend([
+            '--with-precision=%s' % ('double' if '+double' in spec else 'single'),
+            '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
+            '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
+        ])
+        # Activates library support if needed
+        for library in ('metis', 'boost', 'hfd5', 'hypre', 'parmetis'):
+            options.append(
+                '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
+            )
+            if library in spec:
+                options.append(
+                    '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
+                )
+
 
+        configure('--prefix=%s' % prefix, *options)
         # PETSc has its own way of doing parallel make.
         make('MAKE_NP=%s' % make_jobs, parallel=False)
         make("install")
diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py
new file mode 100644
index 0000000000..797772f4f6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/proj/package.py
@@ -0,0 +1,20 @@
+from spack import *
+
+class Proj(Package):
+    """Cartographic Projections"""
+    homepage = "https://github.com/OSGeo/proj.4/wiki"
+    url      = "http://download.osgeo.org/proj/proj-4.9.2.tar.gz"
+
+    version('4.9.2', '9843131676e31bbd903d60ae7dc76cf9')
+    version('4.9.1', '3cbb2a964fd19a496f5f4265a717d31c')
+    version('4.8.0', 'd815838c92a29179298c126effbb1537')
+    version('4.7.0', '927d34623b52e0209ba2bfcca18fe8cd')
+    version('4.6.1', '7dbaab8431ad50c25669fd3fb28dc493')
+
+    # No dependencies
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py
index 8001689a18..f599205644 100644
--- a/var/spack/repos/builtin/packages/py-mpi4py/package.py
+++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py
@@ -5,7 +5,9 @@ class PyMpi4py(Package):
     homepage = "https://pypi.python.org/pypi/mpi4py"
     url      = "https://pypi.python.org/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz"
 
+    version('2.0.0', '4f7d8126d7367c239fd67615680990e3')
     version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c')
+
     extends('python')
     depends_on('py-setuptools')
     depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py
new file mode 100644
index 0000000000..6d10fea74f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-phonopy/package.py
@@ -0,0 +1,18 @@
+from spack import *
+
+class PyPhonopy(Package):
+    """Phonopy is an open source package for phonon
+    calculations at harmonic and quasi-harmonic levels."""
+    homepage = "http://atztogo.github.io/phonopy/index.html"
+    url      = "http://sourceforge.net/projects/phonopy/files/phonopy/phonopy-1.10/phonopy-1.10.0.tar.gz"
+
+    version('1.10.0', '973ed1bcea46e21b9bf747aab9061ff6')
+
+    extends('python')
+    depends_on('py-numpy')
+    depends_on('py-scipy')
+    depends_on('py-matplotlib')
+    depends_on('py-pyyaml')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--home=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py
new file mode 100644
index 0000000000..cae42f6e59
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPyyaml(Package):
+    """PyYAML is a YAML parser and emitter for Python."""
+    homepage = "http://pyyaml.org/wiki/PyYAML"
+    url      = "http://pyyaml.org/download/pyyaml/PyYAML-3.11.tar.gz"
+
+    version('3.11', 'f50e08ef0fe55178479d3a618efe21db')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py
new file mode 100644
index 0000000000..3118e74519
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-wheel/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyWheel(Package):
+    """A built-package format for Python."""
+
+    homepage = "https://pypi.python.org/pypi/wheel"
+    url      = "https://pypi.python.org/packages/source/w/wheel/wheel-0.26.0.tar.gz"
+
+    version('0.26.0', '4cfc6e7e3dc7377d0164914623922a10')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index a1ce06feb0..58d401244e 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -55,6 +55,20 @@ class Python(Package):
         make()
         make("install")
 
+        # Modify compiler paths in configuration files. This is necessary for
+        # building site packages outside of spack
+        filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
+                    (r'\4\5'),
+                    join_path(prefix.lib, 'python%d.%d' % self.version[:2], '_sysconfigdata.py'))
+
+        python3_version = ''
+        if spec.satisfies('@3:'):
+            python3_version = '-%d.%dm' % self.version[:2]
+        makefile_filepath = join_path(prefix.lib, 'python%d.%d' % self.version[:2], 'config%s' % python3_version, 'Makefile')
+        filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
+                    (r'\4\5'),
+                    makefile_filepath)
+
 
     # ========================================================================
     # Set up environment to make install easy for python extensions.
diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py
index f6712ced38..8f7c2f31b1 100644
--- a/var/spack/repos/builtin/packages/qhull/package.py
+++ b/var/spack/repos/builtin/packages/qhull/package.py
@@ -8,20 +8,20 @@ class Qhull(Package):
        implements the Quickhull algorithm for computing the convex
        hull. It handles roundoff errors from floating point
        arithmetic. It computes volumes, surface areas, and
-       approximations to the convex hull.
-
-       Qhull does not support triangulation of non-convex surfaces,
-       mesh generation of non-convex objects, medium-sized inputs in
-       9-D and higher, alpha shapes, weighted Voronoi diagrams,
-       Voronoi volumes, or constrained Delaunay triangulations."""
+       approximations to the convex hull."""
 
     homepage = "http://www.qhull.org"
 
+    version('7.2.0', 'e6270733a826a6a7c32b796e005ec3dc',
+            url="http://www.qhull.org/download/qhull-2015-src-7.2.0.tgz")
+
     version('1.0', 'd0f978c0d8dfb2e919caefa56ea2953c',
             url="http://www.qhull.org/download/qhull-2012.1-src.tgz")
 
     # https://github.com/qhull/qhull/pull/5
-    patch('qhull-iterator.patch')
+    patch('qhull-iterator.patch', when='@1.0')
+    
+    depends_on('cmake')
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index e8d843519d..91afa420c1 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -23,6 +23,7 @@ class Qt(Package):
     version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009',
             url="http://download.qt.io/archive/qt/3/qt-x11-free-3.3.8b.tar.gz")
 
+    variant('mesa', default=False, description='depend on mesa')
     # Add patch for compile issues with qt3 found with use in the OpenSpeedShop project
     variant('krellpatch', default=False, description="build with openspeedshop based patch.")
     patch('qt3krell.patch', when='@3.3.8b+krellpatch')
@@ -48,7 +49,7 @@ class Qt(Package):
     # depends_on("icu4c")
 
     # OpenGL hardware acceleration
-    depends_on("mesa", when='@4:')
+    depends_on("mesa", when='@4:+mesa')
     depends_on("libxcb")
 
 
diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index 9eda11df15..d1aed78e0e 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -1,19 +1,28 @@
 from spack import *
 
 class Silo(Package):
-    """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files."""
+    """Silo is a library for reading and writing a wide variety of scientific
+       data to binary, disk files."""
 
     homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
     url      = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz"
 
-    #version('4.9', 'a83eda4f06761a86726e918fc55e782a')
     version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
 
-    depends_on("hdf5@:1.8.12")
+    variant('fortran', default=True, description='Enable Fortran support')
+
+    depends_on("hdf5")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
-                  "--with-hdf5=%s" %spec['hdf5'].prefix)
+        config_args = [
+            '--enable-fortran' if '+fortran' in spec else '--disable-fortran',
+        ]
+
+        configure(
+            "--prefix=%s" % prefix,
+            "--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
+            "--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
+            *config_args)
 
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py
new file mode 100644
index 0000000000..30c2b76655
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tetgen/package.py
@@ -0,0 +1,28 @@
+from spack import *
+
+class Tetgen(Package):
+    """TetGen is a program and library that can be used to generate tetrahedral
+       meshes for given 3D polyhedral domains. TetGen generates exact constrained
+       Delaunay tetrahedralizations, boundary conforming Delaunay meshes, and
+       Voronoi paritions."""
+
+    homepage = "http://www.tetgen.org"
+    url      = "http://www.tetgen.org/files/tetgen1.4.3.tar.gz"
+
+    version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18')
+
+    # TODO: Make this a build dependency once build dependencies are supported
+    # (see: https://github.com/LLNL/spack/pull/378).
+    depends_on('cmake@2.8.7:', when='@1.5.0:')
+
+    def install(self, spec, prefix):
+        make('tetgen', 'tetlib')
+
+        mkdirp(prefix.bin)
+        install('tetgen', prefix.bin)
+
+        mkdirp(prefix.include)
+        install('tetgen.h', prefix.include)
+
+        mkdirp(prefix.lib)
+        install('libtet.a', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/texinfo/package.py b/var/spack/repos/builtin/packages/texinfo/package.py
index a83c10c0c1..6cf8d79072 100644
--- a/var/spack/repos/builtin/packages/texinfo/package.py
+++ b/var/spack/repos/builtin/packages/texinfo/package.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py
new file mode 100644
index 0000000000..f65d93776d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/triangle/package.py
@@ -0,0 +1,20 @@
+from spack import *
+
+class Triangle(Package):
+    """Triangle is a two-dimensional mesh generator and Delaunay
+       triangulator. Triangle generates exact Delaunay triangulations,
+       constrained Delaunay triangulations, conforming Delaunay
+       triangulations, Voronoi diagrams, and high-quality triangular
+       meshes."""
+
+    homepage = "http://www.cs.cmu.edu/~quake/triangle.html"
+    url      = "http://www.netlib.org/voronoi/triangle.zip"
+
+    version('1.6', '10aff8d7950f5e0e2fb6dd2e340be2c9')
+
+    def install(self, spec, prefix):
+        make()
+        mkdirp(prefix.bin)
+
+        install('triangle', prefix.bin)
+        install('showme', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 7c43f796a4..edc40476e3 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -10,40 +10,44 @@ class Trilinos(Package):
     homepage = "https://trilinos.org/"
     url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz"
 
+    version('12.4.2', '7c830f7f0f68b8ad324690603baf404e')
     version('12.2.1', '6161926ea247863c690e927687f83be9')
     version('12.0.1', 'bd99741d047471e127b8296b2ec08017')
     version('11.14.3', '2f4f83f8333e4233c57d0f01c4b57426')
     version('11.14.2', 'a43590cf896c677890d75bfe75bc6254')
     version('11.14.1', '40febc57f76668be8b6a77b7607bb67f')
 
-    variant('mpi', default=True, description='Add a dependency on MPI and enables MPI dependent packages')
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('debug', default=False, description='Builds a debug version of the libraries')
 
     # Everything should be compiled with -fpic
     depends_on('blas')
     depends_on('lapack')
     depends_on('boost')
-    depends_on('netcdf')
     depends_on('matio')
     depends_on('glm')
     depends_on('swig')
-    depends_on('mpi', when='+mpi')
 
-    def install(self, spec, prefix):
+    # MPI related dependencies
+    depends_on('mpi')
+    depends_on('netcdf+mpi')
+
+    depends_on('python') #  Needs py-numpy activated
 
-        options = [
-            '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
-            '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
-            '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
-            '-DBUILD_SHARED_LIBS:BOOL=ON',
-            '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix,
-            '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix
-        ]
-        if '+mpi' in spec:
-            mpi_options = ['-DTPL_ENABLE_MPI:BOOL=ON']
-            options.extend(mpi_options)
-
-        # -DCMAKE_INSTALL_PREFIX and all the likes...
+    def install(self, spec, prefix):
+        options = []
         options.extend(std_cmake_args)
+
+        options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
+                        '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
+                        '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
+                        '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                        '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
+                        '-DTPL_ENABLE_MPI:STRING=ON',
+                        '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix,
+                        '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix
+                        ])
+
         with working_dir('spack-build', create=True):
             cmake('..', *options)
             make()
diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits2/package.py
new file mode 100644
index 0000000000..9954a733bb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/udunits2/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class Udunits2(Package):
+    """Automated units conversion"""
+
+    homepage = "http://www.unidata.ucar.edu/software/udunits"
+    url      = "ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.20.tar.gz"
+
+    version('2.2.20', '1586b70a49dfe05da5fcc29ef239dce0')
+
+    depends_on('expat')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py
index ba6c9733a7..fdcac95345 100644
--- a/var/spack/repos/builtin/packages/xz/package.py
+++ b/var/spack/repos/builtin/packages/xz/package.py
@@ -8,11 +8,9 @@ class Xz(Package):
     homepage = "http://tukaani.org/xz/"
     url      = "http://tukaani.org/xz/xz-5.2.0.tar.bz2"
 
-    version('5.2.0', '867cc8611760240ebf3440bd6e170bb9',
-            url = 'http://tukaani.org/xz/xz-5.2.0.tar.bz2')
-    version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af',
-            url = 'http://tukaani.org/xz/xz-5.2.2.tar.bz2')
-   
+    version('5.2.0', '867cc8611760240ebf3440bd6e170bb9')
+    version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py
new file mode 100644
index 0000000000..620fe9d456
--- /dev/null
+++ b/var/spack/repos/builtin/packages/zfp/package.py
@@ -0,0 +1,26 @@
+from spack import *
+
+class Zfp(Package):
+    """zfp is an open source C library for compressed floating-point arrays that supports
+       very high throughput read and write random acces, target error bounds or bit rates.
+       Although bit-for-bit lossless compression is not always possible, zfp is usually
+       accurate to within machine epsilon in near-lossless mode, and is often orders of
+       magnitude more accurate than other lossy compressors.
+    """
+
+    homepage = "http://computation.llnl.gov/projects/floating-point-compression"
+    url      = "http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.0.tar.gz"
+
+    version('0.5.0', '2ab29a852e65ad85aae38925c5003654')
+
+    def install(self, spec, prefix):
+        make("shared")
+
+        # No install provided
+        mkdirp(prefix.lib)
+        mkdirp(prefix.include)
+        install('lib/libzfp.so', prefix.lib)
+        install('inc/zfp.h', prefix.include)
+        install('inc/types.h', prefix.include)
+        install('inc/bitstream.h', prefix.include)
+        install('inc/system.h', prefix.include)