Fetch & patch: actually acquire stage lock, and many more issues (#38903)

* Fetching patches wouldn't result in acquiring a stage lock during install
* The installer would acquire a stage lock *after* fetching instead of
   before, leading to races
* The name of the stage for patches was random, so on build failure
   (where stage dirs are not removed), these directories would continue
   to exist after a second successful install.
* There was this redundant "composite fetch" object -- there's already
   a composite stage. Remove this.
* For some reason we do *double* shasum validation of patches, before
   and after compression -- that's just too much? I removed it.

17 files changed, 210 insertions, 219 deletions

diff --git a/lib/spack/spack/cmd/fetch.py b/lib/spack/spack/cmd/fetch.py
index 873c6b54db..227f7e8973 100644
--- a/lib/spack/spack/cmd/fetch.py
+++ b/lib/spack/spack/cmd/fetch.py
@@ -10,6 +10,7 @@ import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.environment as ev
 import spack.repo
+import spack.traverse
 
 description = "fetch archives for packages"
 section = "build"
@@ -36,6 +37,12 @@ def setup_parser(subparser):
 
 
 def fetch(parser, args):
+    if args.no_checksum:
+        spack.config.set("config:checksum", False, scope="command_line")
+
+    if args.deprecated:
+        spack.config.set("config:deprecated", True, scope="command_line")
+
     if args.specs:
         specs = spack.cmd.parse_specs(args.specs, concretize=True)
     else:
@@ -55,18 +62,17 @@ def fetch(parser, args):
         else:
             tty.die("fetch requires at least one spec argument")
 
-    if args.no_checksum:
-        spack.config.set("config:checksum", False, scope="command_line")
+    if args.dependencies or args.missing:
+        to_be_fetched = spack.traverse.traverse_nodes(specs, key=spack.traverse.by_dag_hash)
+    else:
+        to_be_fetched = specs
 
-    if args.deprecated:
-        spack.config.set("config:deprecated", True, scope="command_line")
+    for spec in to_be_fetched:
+        if args.missing and spec.installed:
+            continue
 
-    for spec in specs:
-        if args.missing or args.dependencies:
-            for s in spec.traverse(root=False):
-                # Skip already-installed packages with --missing
-                if args.missing and s.installed:
-                    continue
+        pkg = spec.package
 
-                s.package.do_fetch()
-        spec.package.do_fetch()
+        pkg.stage.keep = True
+        with pkg.stage:
+            pkg.do_fetch()
diff --git a/lib/spack/spack/cmd/patch.py b/lib/spack/spack/cmd/patch.py
index ab51281904..2d2596c9c5 100644
--- a/lib/spack/spack/cmd/patch.py
+++ b/lib/spack/spack/cmd/patch.py
@@ -7,7 +7,11 @@ import llnl.util.tty as tty
 
 import spack.cmd
 import spack.cmd.common.arguments as arguments
+import spack.config
+import spack.environment as ev
+import spack.package_base
 import spack.repo
+import spack.traverse
 
 description = "patch expanded archive sources in preparation for install"
 section = "build"
@@ -21,7 +25,10 @@ def setup_parser(subparser):
 
 def patch(parser, args):
     if not args.specs:
-        tty.die("patch requires at least one spec argument")
+        env = ev.active_environment()
+        if not env:
+            tty.die("`spack patch` requires a spec or an active environment")
+        return _patch_env(env)
 
     if args.no_checksum:
         spack.config.set("config:checksum", False, scope="command_line")
@@ -29,6 +36,19 @@ def patch(parser, args):
     if args.deprecated:
         spack.config.set("config:deprecated", True, scope="command_line")
 
-    specs = spack.cmd.parse_specs(args.specs, concretize=True)
+    specs = spack.cmd.parse_specs(args.specs, concretize=False)
     for spec in specs:
-        spec.package.do_patch()
+        _patch(spack.cmd.matching_spec_from_env(spec).package)
+
+
+def _patch_env(env: ev.Environment):
+    tty.msg(f"Patching specs from environment {env.name}")
+    for spec in spack.traverse.traverse_nodes(env.concrete_roots()):
+        _patch(spec.package)
+
+
+def _patch(pkg: spack.package_base.PackageBase):
+    pkg.stage.keep = True
+    with pkg.stage:
+        pkg.do_patch()
+    tty.msg(f"Patched {pkg.name} in {pkg.stage.path}")
diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index a8d069e6bf..4405ddedca 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -9,9 +9,12 @@ import llnl.util.tty as tty
 
 import spack.cmd
 import spack.cmd.common.arguments as arguments
+import spack.config
 import spack.environment as ev
+import spack.package_base
 import spack.repo
 import spack.stage
+import spack.traverse
 
 description = "expand downloaded archive in preparation for install"
 section = "build"
@@ -27,24 +30,18 @@ def setup_parser(subparser):
 
 
 def stage(parser, args):
-    if not args.specs:
-        env = ev.active_environment()
-        if env:
-            tty.msg("Staging specs from environment %s" % env.name)
-            for spec in env.specs_by_hash.values():
-                for dep in spec.traverse():
-                    dep.package.do_stage()
-                    tty.msg("Staged {0} in {1}".format(dep.package.name, dep.package.stage.path))
-            return
-        else:
-            tty.die("`spack stage` requires a spec or an active environment")
-
     if args.no_checksum:
         spack.config.set("config:checksum", False, scope="command_line")
 
     if args.deprecated:
         spack.config.set("config:deprecated", True, scope="command_line")
 
+    if not args.specs:
+        env = ev.active_environment()
+        if not env:
+            tty.die("`spack stage` requires a spec or an active environment")
+        return _stage_env(env)
+
     specs = spack.cmd.parse_specs(args.specs, concretize=False)
 
     # We temporarily modify the working directory when setting up a stage, so we need to
@@ -57,7 +54,24 @@ def stage(parser, args):
 
     for spec in specs:
         spec = spack.cmd.matching_spec_from_env(spec)
+        pkg = spec.package
+
         if custom_path:
-            spec.package.path = custom_path
-        spec.package.do_stage()
-        tty.msg("Staged {0} in {1}".format(spec.package.name, spec.package.stage.path))
+            pkg.path = custom_path
+
+        _stage(pkg)
+
+
+def _stage_env(env: ev.Environment):
+    tty.msg(f"Staging specs from environment {env.name}")
+    for spec in spack.traverse.traverse_nodes(env.concrete_roots()):
+        _stage(spec.package)
+
+
+def _stage(pkg: spack.package_base.PackageBase):
+    # Use context manager to ensure we don't restage while an installation is in progress
+    # keep = True ensures that the stage is not removed after exiting the context manager
+    pkg.stage.keep = True
+    with pkg.stage:
+        pkg.do_stage()
+    tty.msg(f"Staged {pkg.name} in {pkg.stage.path}")
diff --git a/lib/spack/spack/environment/environment.py b/lib/spack/spack/environment/environment.py
index 79268321fb..feb3747770 100644
--- a/lib/spack/spack/environment/environment.py
+++ b/lib/spack/spack/environment/environment.py
@@ -29,6 +29,7 @@ import spack.compilers
 import spack.concretize
 import spack.config
 import spack.error
+import spack.fetch_strategy
 import spack.hash_types as ht
 import spack.hooks
 import spack.main
@@ -1265,12 +1266,12 @@ class Environment:
             # We construct a package class ourselves, rather than asking for
             # Spec.package, since Spec only allows this when it is concrete
             package = pkg_cls(spec)
-            if isinstance(package.fetcher[0], spack.fetch_strategy.GitFetchStrategy):
-                package.fetcher[0].get_full_repo = True
+            if isinstance(package.fetcher, spack.fetch_strategy.GitFetchStrategy):
+                package.fetcher.get_full_repo = True
                 # If we retrieved this version before and cached it, we may have
                 # done so without cloning the full git repo; likewise, any
                 # mirror might store an instance with truncated history.
-                package.stage[0].disable_mirrors()
+                package.stage.disable_mirrors()
 
             package.stage.steal_source(abspath)
 
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 077a5d2ae4..f440ea94b7 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -42,7 +42,6 @@ import spack.error
 import spack.url
 import spack.util.crypto as crypto
 import spack.util.git
-import spack.util.pattern as pattern
 import spack.util.url as url_util
 import spack.util.web as web_util
 import spack.version
@@ -228,24 +227,6 @@ class BundleFetchStrategy(FetchStrategy):
         """BundlePackages don't have a mirror id."""
 
 
-class FetchStrategyComposite(pattern.Composite):
-    """Composite for a FetchStrategy object."""
-
-    matches = FetchStrategy.matches
-
-    def __init__(self):
-        super().__init__(["fetch", "check", "expand", "reset", "archive", "cachable", "mirror_id"])
-
-    def source_id(self):
-        component_ids = tuple(i.source_id() for i in self)
-        if all(component_ids):
-            return component_ids
-
-    def set_package(self, package):
-        for item in self:
-            item.package = package
-
-
 @fetcher
 class URLFetchStrategy(FetchStrategy):
     """URLFetchStrategy pulls source code from a URL for an archive, check the
@@ -488,17 +469,7 @@ class URLFetchStrategy(FetchStrategy):
         if not self.digest:
             raise NoDigestError("Attempt to check URLFetchStrategy with no digest.")
 
-        checker = crypto.Checker(self.digest)
-        if not checker.check(self.archive_file):
-            # On failure, provide some information about the file size and
-            # contents, so that we can quickly see what the issue is (redirect
-            # was not followed, empty file, text instead of binary, ...)
-            size, contents = fs.filesummary(self.archive_file)
-            raise ChecksumError(
-                f"{checker.hash_name} checksum failed for {self.archive_file}",
-                f"Expected {self.digest} but got {checker.sum}. "
-                f"File size = {size} bytes. Contents = {contents!r}",
-            )
+        verify_checksum(self.archive_file, self.digest)
 
     @_needs_stage
     def reset(self):
@@ -1388,6 +1359,45 @@ class GCSFetchStrategy(URLFetchStrategy):
             raise FailedDownloadError(self.url)
 
 
+@fetcher
+class FetchAndVerifyExpandedFile(URLFetchStrategy):
+    """Fetch strategy that verifies the content digest during fetching,
+    as well as after expanding it."""
+
+    def __init__(self, url, archive_sha256: str, expanded_sha256: str):
+        super().__init__(url, archive_sha256)
+        self.expanded_sha256 = expanded_sha256
+
+    def expand(self):
+        """Verify checksum after expanding the archive."""
+
+        # Expand the archive
+        super().expand()
+
+        # Ensure a single patch file.
+        src_dir = self.stage.source_path
+        files = os.listdir(src_dir)
+
+        if len(files) != 1:
+            raise ChecksumError(self, f"Expected a single file in {src_dir}.")
+
+        verify_checksum(os.path.join(src_dir, files[0]), self.expanded_sha256)
+
+
+def verify_checksum(file, digest):
+    checker = crypto.Checker(digest)
+    if not checker.check(file):
+        # On failure, provide some information about the file size and
+        # contents, so that we can quickly see what the issue is (redirect
+        # was not followed, empty file, text instead of binary, ...)
+        size, contents = fs.filesummary(file)
+        raise ChecksumError(
+            f"{checker.hash_name} checksum failed for {file}",
+            f"Expected {digest} but got {checker.sum}. "
+            f"File size = {size} bytes. Contents = {contents!r}",
+        )
+
+
 def stable_target(fetcher):
     """Returns whether the fetcher target is expected to have a stable
     checksum. This is only true if the target is a preexisting archive
diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py
index 4b352d9293..92d12e04cb 100644
--- a/lib/spack/spack/installer.py
+++ b/lib/spack/spack/installer.py
@@ -2341,28 +2341,28 @@ class BuildProcessInstaller:
     def run(self) -> bool:
         """Main entry point from ``build_process`` to kick off install in child."""
 
-        self.timer.start("stage")
+        self.pkg.stage.keep = self.keep_stage
 
-        if not self.fake:
-            if not self.skip_patch:
-                self.pkg.do_patch()
-            else:
-                self.pkg.do_stage()
+        with self.pkg.stage:
+            self.timer.start("stage")
 
-        self.timer.stop("stage")
+            if not self.fake:
+                if not self.skip_patch:
+                    self.pkg.do_patch()
+                else:
+                    self.pkg.do_stage()
 
-        tty.debug(
-            "{0} Building {1} [{2}]".format(self.pre, self.pkg_id, self.pkg.build_system_class)  # type: ignore[attr-defined] # noqa: E501
-        )
+            self.timer.stop("stage")
 
-        # get verbosity from do_install() parameter or saved value
-        self.echo = self.verbose
-        if spack.package_base.PackageBase._verbose is not None:
-            self.echo = spack.package_base.PackageBase._verbose
+            tty.debug(
+                "{0} Building {1} [{2}]".format(self.pre, self.pkg_id, self.pkg.build_system_class)  # type: ignore[attr-defined] # noqa: E501
+            )
 
-        self.pkg.stage.keep = self.keep_stage
+            # get verbosity from do_install() parameter or saved value
+            self.echo = self.verbose
+            if spack.package_base.PackageBase._verbose is not None:
+                self.echo = spack.package_base.PackageBase._verbose
 
-        with self.pkg.stage:
             # Run the pre-install hook in the child process after
             # the directory is created.
             spack.hooks.pre_install(self.pkg.spec)
diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py
index d6be146291..3c27fdbd90 100644
--- a/lib/spack/spack/mirror.py
+++ b/lib/spack/spack/mirror.py
@@ -675,12 +675,9 @@ def create_mirror_from_package_object(pkg_obj, mirror_cache, mirror_stats):
     num_retries = 3
     while num_retries > 0:
         try:
+            # Includes patches and resources
             with pkg_obj.stage as pkg_stage:
                 pkg_stage.cache_mirror(mirror_cache, mirror_stats)
-                for patch in pkg_obj.all_patches():
-                    if patch.stage:
-                        patch.stage.cache_mirror(mirror_cache, mirror_stats)
-                    patch.clean()
             exception = None
             break
         except Exception as e:
diff --git a/lib/spack/spack/package_base.py b/lib/spack/spack/package_base.py
index 370f90aff8..bbeeef1923 100644
--- a/lib/spack/spack/package_base.py
+++ b/lib/spack/spack/package_base.py
@@ -44,6 +44,7 @@ import spack.hooks
 import spack.mirror
 import spack.mixins
 import spack.multimethod
+import spack.patch
 import spack.paths
 import spack.repo
 import spack.spec
@@ -62,7 +63,7 @@ from spack.install_test import (
     install_test_root,
 )
 from spack.installer import InstallError, PackageInstaller
-from spack.stage import ResourceStage, Stage, StageComposite, compute_stage_name
+from spack.stage import DIYStage, ResourceStage, Stage, StageComposite, compute_stage_name
 from spack.util.executable import ProcessError, which
 from spack.util.package_hash import package_hash
 from spack.util.web import FetchError
@@ -981,20 +982,17 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
 
         return None
 
-    def _make_resource_stage(self, root_stage, fetcher, resource):
-        resource_stage_folder = self._resource_stage(resource)
-        mirror_paths = spack.mirror.mirror_archive_paths(
-            fetcher, os.path.join(self.name, "%s-%s" % (resource.name, self.version))
-        )
-        stage = ResourceStage(
+    def _make_resource_stage(self, root_stage, resource):
+        return ResourceStage(
             resource.fetcher,
             root=root_stage,
             resource=resource,
-            name=resource_stage_folder,
-            mirror_paths=mirror_paths,
+            name=self._resource_stage(resource),
+            mirror_paths=spack.mirror.mirror_archive_paths(
+                resource.fetcher, os.path.join(self.name, f"{resource.name}-{self.version}")
+            ),
             path=self.path,
         )
-        return stage
 
     def _download_search(self):
         dynamic_fetcher = fs.from_list_url(self)
@@ -1003,7 +1001,7 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
     def _make_root_stage(self, fetcher):
         # Construct a mirror path (TODO: get this out of package.py)
         mirror_paths = spack.mirror.mirror_archive_paths(
-            fetcher, os.path.join(self.name, "%s-%s" % (self.name, self.version)), self.spec
+            fetcher, os.path.join(self.name, f"{self.name}-{self.version}"), self.spec
         )
         # Construct a path where the stage should build..
         s = self.spec
@@ -1021,24 +1019,21 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
         # If it's a dev package (not transitively), use a DIY stage object
         dev_path_var = self.spec.variants.get("dev_path", None)
         if dev_path_var:
-            return spack.stage.DIYStage(dev_path_var.value)
-
-        # 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)
+            return DIYStage(dev_path_var.value)
 
-        return composite_stage
+        # To fetch the current version
+        source_stage = self._make_root_stage(self.fetcher)
+
+        # Extend it with all resources and patches
+        all_stages = StageComposite()
+        all_stages.append(source_stage)
+        all_stages.extend(
+            self._make_resource_stage(source_stage, r) for r in self._get_needed_resources()
+        )
+        all_stages.extend(
+            p.stage for p in self.spec.patches if isinstance(p, spack.patch.UrlPatch)
+        )
+        return all_stages
 
     @property
     def stage(self):
@@ -1187,26 +1182,12 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
         warnings.warn(msg)
         return self.spec.installed_upstream
 
-    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)
-        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)
-        fetcher.set_package(self)
-        return fetcher
-
     @property
     def fetcher(self):
         if not self.spec.versions.concrete:
             raise ValueError("Cannot retrieve fetcher for package without concrete version.")
         if not self._fetcher:
-            self._fetcher = self._make_fetcher()
+            self._fetcher = fs.for_package_version(self)
         return self._fetcher
 
     @fetcher.setter
@@ -1445,11 +1426,6 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
 
         self.stage.cache_local()
 
-        for patch in self.spec.patches:
-            patch.fetch()
-            if patch.stage:
-                patch.stage.cache_local()
-
     def do_stage(self, mirror_only=False):
         """Unpacks and expands the fetched tarball."""
         # Always create the stage directory at this point.  Why?  A no-code
@@ -2341,9 +2317,6 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
 
     def do_clean(self):
         """Removes the package's build stage and source tarball."""
-        for patch in self.spec.patches:
-            patch.clean()
-
         self.stage.destroy()
 
     @classmethod
diff --git a/lib/spack/spack/patch.py b/lib/spack/spack/patch.py
index e761102d2b..3742131fe2 100644
--- a/lib/spack/spack/patch.py
+++ b/lib/spack/spack/patch.py
@@ -15,6 +15,7 @@ import llnl.util.lang
 import spack
 import spack.error
 import spack.fetch_strategy as fs
+import spack.mirror
 import spack.repo
 import spack.stage
 import spack.util.spack_json as sjson
@@ -75,22 +76,14 @@ class Patch:
         self.level = level
         self.working_dir = working_dir
 
-    def fetch(self):
-        """Fetch the patch in case of a UrlPatch"""
-
-    def clean(self):
-        """Clean up the patch stage in case of a UrlPatch"""
-
-    def apply(self, stage):
+    def apply(self, stage: spack.stage.Stage):
         """Apply a patch to source in a stage.
 
         Arguments:
             stage (spack.stage.Stage): stage where source code lives
         """
-        assert self.path, "Path for patch not set in apply: %s" % self.path_or_url
-
-        if not os.path.isfile(self.path):
-            raise NoSuchPatchError("No such patch: %s" % self.path)
+        if not self.path or not os.path.isfile(self.path):
+            raise NoSuchPatchError(f"No such patch: {self.path}")
 
         apply_patch(stage, self.path, self.level, self.working_dir)
 
@@ -197,70 +190,44 @@ class UrlPatch(Patch):
         if not self.sha256:
             raise PatchDirectiveError("URL patches require a sha256 checksum")
 
-    def fetch(self):
-        """Retrieve the patch in a temporary stage and compute self.path
+    def apply(self, stage: spack.stage.Stage):
+        assert self.stage.expanded, "Stage must be expanded before applying patches"
 
-        Args:
-            stage: stage for the package that needs to be patched
-        """
-        self.stage.create()
-        self.stage.fetch()
-        self.stage.check()
+        # Get the patch file.
+        files = os.listdir(self.stage.source_path)
+        assert len(files) == 1, "Expected one file in stage source path, found %s" % files
+        self.path = os.path.join(self.stage.source_path, files[0])
 
-        root = self.stage.path
-        if self.archive_sha256:
-            self.stage.expand_archive()
-            root = self.stage.source_path
-
-        files = os.listdir(root)
-        if not files:
-            if self.archive_sha256:
-                raise NoSuchPatchError("Archive was empty: %s" % self.url)
-            else:
-                raise NoSuchPatchError("Patch failed to download: %s" % self.url)
-
-        self.path = os.path.join(root, files.pop())
-
-        if not os.path.isfile(self.path):
-            raise NoSuchPatchError("Archive %s contains no patch file!" % self.url)
-
-        # for a compressed archive, Need to check the patch sha256 again
-        # and the patch is in a directory, not in the same place
-        if self.archive_sha256 and spack.config.get("config:checksum"):
-            checker = Checker(self.sha256)
-            if not checker.check(self.path):
-                raise fs.ChecksumError(
-                    "sha256 checksum failed for %s" % self.path,
-                    "Expected %s but got %s" % (self.sha256, checker.sum),
-                )
+        return super().apply(stage)
 
     @property
     def stage(self):
         if self._stage:
             return self._stage
 
-        # use archive digest for compressed archives
-        fetch_digest = self.sha256
-        if self.archive_sha256:
-            fetch_digest = self.archive_sha256
+        fetch_digest = self.archive_sha256 or self.sha256
 
-        fetcher = fs.URLFetchStrategy(self.url, fetch_digest, expand=bool(self.archive_sha256))
+        # Two checksums, one for compressed file, one for its contents
+        if self.archive_sha256:
+            fetcher = fs.FetchAndVerifyExpandedFile(
+                self.url, archive_sha256=self.archive_sha256, expanded_sha256=self.sha256
+            )
+        else:
+            fetcher = fs.URLFetchStrategy(self.url, sha256=self.sha256, expand=False)
 
         # The same package can have multiple patches with the same name but
         # with different contents, therefore apply a subset of the hash.
         name = "{0}-{1}".format(os.path.basename(self.url), fetch_digest[:7])
 
         per_package_ref = os.path.join(self.owner.split(".")[-1], name)
-        # Reference starting with "spack." is required to avoid cyclic imports
         mirror_ref = spack.mirror.mirror_archive_paths(fetcher, per_package_ref)
-
-        self._stage = spack.stage.Stage(fetcher, mirror_paths=mirror_ref)
-        self._stage.create()
+        self._stage = spack.stage.Stage(
+            fetcher,
+            name=f"{spack.stage.stage_prefix}patch-{fetch_digest}",
+            mirror_paths=mirror_ref,
+        )
         return self._stage
 
-    def clean(self):
-        self.stage.destroy()
-
     def to_dict(self):
         data = super().to_dict()
         data["url"] = self.url
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index 5049312e47..511b487393 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -50,7 +50,7 @@ stage_prefix = "spack-stage-"
 
 def compute_stage_name(spec):
     """Determine stage name given a spec"""
-    default_stage_structure = "spack-stage-{name}-{version}-{hash}"
+    default_stage_structure = stage_prefix + "{name}-{version}-{hash}"
     stage_name_structure = spack.config.get("config:stage_name", default=default_stage_structure)
     return spec.format(format_string=stage_name_structure)
 
@@ -744,6 +744,7 @@ class StageComposite(pattern.Composite):
                 "cache_local",
                 "cache_mirror",
                 "steal_source",
+                "disable_mirrors",
                 "managed_by_spack",
             ]
         )
diff --git a/lib/spack/spack/test/cmd/stage.py b/lib/spack/spack/test/cmd/stage.py
index 9fff89afb4..8b28b55116 100644
--- a/lib/spack/spack/test/cmd/stage.py
+++ b/lib/spack/spack/test/cmd/stage.py
@@ -10,8 +10,11 @@ import pytest
 
 import spack.config
 import spack.environment as ev
+import spack.package_base
 import spack.repo
-from spack.main import SpackCommand
+import spack.stage
+import spack.traverse
+from spack.main import SpackCommand, SpackCommandError
 from spack.version import Version
 
 stage = SpackCommand("stage")
@@ -21,6 +24,7 @@ pytestmark = pytest.mark.usefixtures("install_mockery", "mock_packages")
 
 
 @pytest.mark.skipif(sys.platform == "win32", reason="not implemented on windows")
+@pytest.mark.disable_clean_stage_check
 def test_stage_spec(monkeypatch):
     """Verify that staging specs works."""
 
@@ -56,11 +60,12 @@ def test_stage_path(check_stage_path):
 
 def test_stage_path_errors_multiple_specs(check_stage_path):
     """Verify that --path only works with single specs."""
-    with pytest.raises(spack.main.SpackCommandError):
-        stage("--path={0}".format(check_stage_path), "trivial-install-test-package", "mpileaks")
+    with pytest.raises(SpackCommandError):
+        stage(f"--path={check_stage_path}", "trivial-install-test-package", "mpileaks")
 
 
 @pytest.mark.skipif(sys.platform == "win32", reason="not implemented on windows")
+@pytest.mark.disable_clean_stage_check
 def test_stage_with_env_outside_env(mutable_mock_env_path, monkeypatch):
     """Verify that stage concretizes specs not in environment instead of erroring."""
 
@@ -79,6 +84,7 @@ def test_stage_with_env_outside_env(mutable_mock_env_path, monkeypatch):
 
 
 @pytest.mark.skipif(sys.platform == "win32", reason="not implemented on windows")
+@pytest.mark.disable_clean_stage_check
 def test_stage_with_env_inside_env(mutable_mock_env_path, monkeypatch):
     """Verify that stage filters specs in environment instead of reconcretizing."""
 
@@ -97,6 +103,7 @@ def test_stage_with_env_inside_env(mutable_mock_env_path, monkeypatch):
 
 
 @pytest.mark.skipif(sys.platform == "win32", reason="not implemented on windows")
+@pytest.mark.disable_clean_stage_check
 def test_stage_full_env(mutable_mock_env_path, monkeypatch):
     """Verify that stage filters specs in environment."""
 
@@ -105,10 +112,7 @@ def test_stage_full_env(mutable_mock_env_path, monkeypatch):
     e.concretize()
 
     # list all the package names that should be staged
-    expected = set()
-    for spec in e.specs_by_hash.values():
-        for dep in spec.traverse():
-            expected.add(dep.name)
+    expected = set(dep.name for dep in spack.traverse.traverse_nodes(e.concrete_roots()))
 
     # pop the package name from the list instead of actually staging
     def fake_stage(pkg, mirror_only=False):
diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py
index 457aa4af00..2d174316b0 100644
--- a/lib/spack/spack/test/concretize_preferences.py
+++ b/lib/spack/spack/test/concretize_preferences.py
@@ -178,11 +178,11 @@ class TestConcretizePreferences:
             {"url": "http://www.somewhereelse.com/mpileaks-1.0.tar.gz"},
         )
         spec = concretize("mpileaks")
-        assert spec.package.fetcher[0].url == "http://www.somewhereelse.com/mpileaks-2.3.tar.gz"
+        assert spec.package.fetcher.url == "http://www.somewhereelse.com/mpileaks-2.3.tar.gz"
 
         update_packages("mpileaks", "package_attributes", {})
         spec = concretize("mpileaks")
-        assert spec.package.fetcher[0].url == "http://www.llnl.gov/mpileaks-2.3.tar.gz"
+        assert spec.package.fetcher.url == "http://www.llnl.gov/mpileaks-2.3.tar.gz"
 
     def test_config_set_pkg_property_new(self, mutable_mock_repo):
         """Test that you can set arbitrary attributes on the Package class"""
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index 6776c7db87..e75585b0db 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -50,7 +50,7 @@ import spack.util.git
 import spack.util.gpg
 import spack.util.spack_yaml as syaml
 import spack.util.url as url_util
-from spack.fetch_strategy import FetchStrategyComposite, URLFetchStrategy
+from spack.fetch_strategy import URLFetchStrategy
 from spack.util.pattern import Bunch
 from spack.util.web import FetchError
 
@@ -993,10 +993,9 @@ def install_mockery_mutable_config(temporary_store, mutable_config, mock_package
 @pytest.fixture()
 def mock_fetch(mock_archive, monkeypatch):
     """Fake the URL for a package so it downloads from a file."""
-    mock_fetcher = FetchStrategyComposite()
-    mock_fetcher.append(URLFetchStrategy(mock_archive.url))
-
-    monkeypatch.setattr(spack.package_base.PackageBase, "fetcher", mock_fetcher)
+    monkeypatch.setattr(
+        spack.package_base.PackageBase, "fetcher", URLFetchStrategy(mock_archive.url)
+    )
 
 
 class MockLayout:
diff --git a/lib/spack/spack/test/installer.py b/lib/spack/spack/test/installer.py
index 49840814a0..a937f8f770 100644
--- a/lib/spack/spack/test/installer.py
+++ b/lib/spack/spack/test/installer.py
@@ -20,6 +20,7 @@ import spack.compilers
 import spack.concretize
 import spack.config
 import spack.installer as inst
+import spack.package_base
 import spack.package_prefs as prefs
 import spack.repo
 import spack.spec
@@ -1139,6 +1140,7 @@ def _test_install_fail_fast_on_except_patch(installer, **kwargs):
     raise RuntimeError("mock patch failure")
 
 
+@pytest.mark.disable_clean_stage_check
 def test_install_fail_fast_on_except(install_mockery, monkeypatch, capsys):
     """Test fail_fast install when an install failure results from an error."""
     const_arg = installer_args(["a"], {"fail_fast": True})
diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py
index 0ed89322c1..7afe8df6ac 100644
--- a/lib/spack/spack/test/mirror.py
+++ b/lib/spack/spack/test/mirror.py
@@ -65,7 +65,7 @@ def check_mirror():
             assert os.path.isdir(mirror_root)
 
             for spec in specs:
-                fetcher = spec.package.fetcher[0]
+                fetcher = spec.package.fetcher
                 per_package_ref = os.path.join(spec.name, "-".join([spec.name, str(spec.version)]))
                 mirror_paths = spack.mirror.mirror_archive_paths(fetcher, per_package_ref)
                 expected_path = os.path.join(mirror_root, mirror_paths.storage_path)
diff --git a/lib/spack/spack/test/packaging.py b/lib/spack/spack/test/packaging.py
index c47a0d6c46..bd0a89a4de 100644
--- a/lib/spack/spack/test/packaging.py
+++ b/lib/spack/spack/test/packaging.py
@@ -26,7 +26,7 @@ import spack.repo
 import spack.store
 import spack.util.gpg
 import spack.util.url as url_util
-from spack.fetch_strategy import FetchStrategyComposite, URLFetchStrategy
+from spack.fetch_strategy import URLFetchStrategy
 from spack.paths import mock_gpg_keys_path
 from spack.relocate import (
     macho_find_paths,
@@ -46,9 +46,7 @@ pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="does not run on
 def test_buildcache(mock_archive, tmp_path, monkeypatch, mutable_config):
     # Install a test package
     spec = Spec("trivial-install-test-package").concretized()
-    fetcher = FetchStrategyComposite()
-    fetcher.append(URLFetchStrategy(mock_archive.url))
-    monkeypatch.setattr(spec.package, "fetcher", fetcher)
+    monkeypatch.setattr(spec.package, "fetcher", URLFetchStrategy(mock_archive.url))
     spec.package.do_install()
     pkghash = "/" + str(spec.dag_hash(7))
 
@@ -485,8 +483,7 @@ def mock_download():
                 "<non-existent URL>", "This FetchStrategy always fails"
             )
 
-    fetcher = FetchStrategyComposite()
-    fetcher.append(FailedDownloadStrategy())
+    fetcher = FailedDownloadStrategy()
 
     @property
     def fake_fn(self):
@@ -532,9 +529,7 @@ def fetching_not_allowed(monkeypatch):
         def fetch(self):
             raise Exception("Sources are fetched but shouldn't have been")
 
-    fetcher = FetchStrategyComposite()
-    fetcher.append(FetchingNotAllowed())
-    monkeypatch.setattr(spack.package_base.PackageBase, "fetcher", fetcher)
+    monkeypatch.setattr(spack.package_base.PackageBase, "fetcher", FetchingNotAllowed())
 
 
 def test_fetch_without_code_is_noop(
diff --git a/lib/spack/spack/test/patch.py b/lib/spack/spack/test/patch.py
index 1be3f44b18..a6e964353b 100644
--- a/lib/spack/spack/test/patch.py
+++ b/lib/spack/spack/test/patch.py
@@ -115,9 +115,11 @@ third line
 """
                 )
         # apply the patch and compare files
-        patch.fetch()
-        patch.apply(stage)
-        patch.clean()
+        with patch.stage:
+            patch.stage.create()
+            patch.stage.fetch()
+            patch.stage.expand_archive()
+            patch.apply(stage)
 
         with working_dir(stage.source_path):
             assert filecmp.cmp("foo.txt", "foo-expected.txt")