Merge branch 'baserock/richardmaw/S8717/refactor-petrify-v4'

Reviewed-by: Lars Wirzenius
Reviewed-by: Daniel Silverstone

Daniel gave his +1 with the caveat that he would like tests for
petrifying a system branch other than master.

14 files changed, 495 insertions, 22 deletions

diff --git a/morphlib/__init__.py b/morphlib/__init__.py
index bcdd733b..b1e3c7c3 100644
--- a/morphlib/__init__.py
+++ b/morphlib/__init__.py
@@ -65,6 +65,7 @@ import localrepocache
 import mountableimage
 import morph2
 import morphologyfactory
+import morphologyfinder
 import morph3
 import morphloader
 import morphset
diff --git a/morphlib/git.py b/morphlib/git.py
index 4ff08a72..27146206 100644
--- a/morphlib/git.py
+++ b/morphlib/git.py
@@ -20,6 +20,7 @@ import ConfigParser
 import logging
 import os
 import re
+import string
 import StringIO
 import time
 
@@ -311,8 +312,7 @@ def clone_into(runcmd, srcpath, targetpath, ref=None):
 def is_valid_sha1(ref):
     '''Checks whether a string is a valid SHA1.'''
 
-    valid_chars = 'abcdefABCDEF0123456789'
-    return len(ref) == 40 and all([x in valid_chars for x in ref])
+    return len(ref) == 40 and all(x in string.hexdigits for x in ref)
 
 def rev_parse(runcmd, gitdir, ref):
     '''Find the sha1 for the given ref'''
diff --git a/morphlib/gitdir.py b/morphlib/gitdir.py
index f40190ff..cb247303 100644
--- a/morphlib/gitdir.py
+++ b/morphlib/gitdir.py
@@ -17,10 +17,27 @@
 
 
 import cliapp
+import glob
+import os
 
 import morphlib
 
 
+class NoWorkingTreeError(cliapp.AppException):
+
+    def __init__(self, repo):
+        cliapp.AppException.__init__(
+            self, 'Git directory %s has no working tree '
+                  '(is bare).' % repo.dirname)
+
+
+class InvalidRefError(cliapp.AppException):
+    def __init__(self, repo, ref):
+        cliapp.AppException.__init__(
+            self, 'Git directory %s has no commit '
+                  'at ref %s.' %(repo.dirname, ref))
+
+
 class GitDirectory(object):
 
     '''Represent a git working tree + .git directory.
@@ -126,6 +143,58 @@ class GitDirectory(object):
         '''Run "git remote update --prune".'''
         self._runcmd(['git', 'remote', 'update', '--prune'])
 
+    def is_bare(self):
+        '''Determine whether the repository has no work tree (is bare)'''
+        return self.get_config('core.bare') == 'true'
+
+    def list_files(self, ref=None):
+        '''Return an iterable of the files in the repository.
+
+        If `ref` is specified, list files at that ref, otherwise
+        use the working tree.
+
+        If this is a bare repository and no ref is specified, raises
+        an exception.
+
+        '''
+        if ref is None and self.is_bare():
+            raise NoWorkingTreeError(self)
+        if ref is None:
+            return self._list_files_in_work_tree()
+        else:
+            return self._list_files_in_ref(ref)
+
+    def _rev_parse_tree(self, ref):
+        try:
+            return self._runcmd(['git', 'rev-parse', '--verify',
+                                 '%s^{tree}' % ref]).strip()
+        except cliapp.AppException as e:
+            raise InvalidRefError(self, ref)
+
+    def _list_files_in_work_tree(self):
+        for dirpath, subdirs, filenames in os.walk(self.dirname):
+            if dirpath == self.dirname and '.git' in subdirs:
+                subdirs.remove('.git')
+            for filename in filenames:
+                yield os.path.join(dirpath, filename)[len(self.dirname)+1:]
+
+    def _list_files_in_ref(self, ref):
+        tree = self._rev_parse_tree(ref)
+        output = self._runcmd(['git', 'ls-tree', '--name-only', '-rz', tree])
+        # ls-tree appends \0 instead of interspersing, so we need to
+        # strip the trailing \0 before splitting
+        paths = output.strip('\0').split('\0')
+        return paths
+
+    def read_file(self, filename, ref=None):
+        if ref is None and self.is_bare():
+            raise NoWorkingTreeError(self)
+        if ref is None:
+            with open(os.path.join(self.dirname, filename)) as f:
+                return f.read()
+        tree = self._rev_parse_tree(ref)
+        return self.cat_file('blob', tree, filename)
+
 
 def init(dirname):
     '''Initialise a new git repository.'''
diff --git a/morphlib/gitdir_tests.py b/morphlib/gitdir_tests.py
index 2494981a..175b8ee7 100644
--- a/morphlib/gitdir_tests.py
+++ b/morphlib/gitdir_tests.py
@@ -64,3 +64,76 @@ class GitDirectoryTests(unittest.TestCase):
         gitdir.set_remote_fetch_url('origin', url)
         self.assertEqual(gitdir.get_remote_fetch_url('origin'), url)
 
+class GitDirectoryContentsTests(unittest.TestCase):
+
+    def setUp(self):
+        self.tempdir = tempfile.mkdtemp()
+        self.dirname = os.path.join(self.tempdir, 'foo')
+        os.mkdir(self.dirname)
+        gd = morphlib.gitdir.init(self.dirname)
+        for fn in ('foo', 'bar.morph', 'baz.morph', 'quux'):
+            with open(os.path.join(self.dirname, fn), "w") as f:
+                f.write('dummy morphology text')
+        gd._runcmd(['git', 'add', '.'])
+        gd._runcmd(['git', 'commit', '-m', 'Initial commit'])
+        os.rename(os.path.join(self.dirname, 'foo'),
+                  os.path.join(self.dirname, 'foo.morph'))
+        self.mirror = os.path.join(self.tempdir, 'mirror')
+        gd._runcmd(['git', 'clone', '--mirror', self.dirname, self.mirror])
+
+    def tearDown(self):
+        shutil.rmtree(self.tempdir)
+
+    def test_lists_files_in_work_tree(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        self.assertEqual(sorted(gd.list_files()),
+                         ['bar.morph', 'baz.morph', 'foo.morph', 'quux'])
+
+    def test_read_file_in_work_tree(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        self.assertEqual(gd.read_file('bar.morph'),
+                         'dummy morphology text')
+
+    def test_list_raises_no_ref_no_work_tree(self):
+        gd = morphlib.gitdir.GitDirectory(self.mirror)
+        self.assertRaises(morphlib.gitdir.NoWorkingTreeError,
+                          gd.list_files)
+
+    def test_read_raises_no_ref_no_work_tree(self):
+        gd = morphlib.gitdir.GitDirectory(self.mirror)
+        self.assertRaises(morphlib.gitdir.NoWorkingTreeError,
+                          gd.read_file, 'bar.morph')
+
+    def test_lists_files_in_HEAD(self):
+        for gitdir in (self.dirname, self.mirror):
+            gd = morphlib.gitdir.GitDirectory(gitdir)
+            self.assertEqual(sorted(gd.list_files('HEAD')),
+                             ['bar.morph', 'baz.morph', 'foo', 'quux'])
+
+    def test_read_files_in_HEAD(self):
+        for gitdir in (self.dirname, self.mirror):
+            gd = morphlib.gitdir.GitDirectory(gitdir)
+            self.assertEqual(gd.read_file('bar.morph', 'HEAD'),
+                             'dummy morphology text')
+
+    def test_lists_files_in_named_ref(self):
+        for gitdir in (self.dirname, self.mirror):
+            gd = morphlib.gitdir.GitDirectory(gitdir)
+            self.assertEqual(sorted(gd.list_files('master')),
+                             ['bar.morph', 'baz.morph', 'foo', 'quux'])
+
+    def test_read_file_in_named_ref(self):
+        for gitdir in (self.dirname, self.mirror):
+            gd = morphlib.gitdir.GitDirectory(gitdir)
+            self.assertEqual(gd.read_file('bar.morph', 'master'),
+                             'dummy morphology text')
+
+    def test_list_raises_invalid_ref(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        self.assertRaises(morphlib.gitdir.InvalidRefError,
+                          gd.list_files, 'no-such-ref')
+
+    def test_read_raises_invalid_ref(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        self.assertRaises(morphlib.gitdir.InvalidRefError,
+                          gd.read_file, 'bar', 'no-such-ref')
diff --git a/morphlib/morphologyfinder.py b/morphlib/morphologyfinder.py
new file mode 100644
index 00000000..affa0e97
--- /dev/null
+++ b/morphlib/morphologyfinder.py
@@ -0,0 +1,71 @@
+# Copyright (C) 2013  Codethink Limited
+#
+# 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 of the License.
+#
+# 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
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# =*= License: GPL-2 =*=
+
+
+import cliapp
+
+import morphlib
+
+
+class MorphologyFinder(object):
+
+    '''Abstract away finding morphologies in a git repository.
+
+    This class provides an abstraction layer between a git repository
+    and the morphologies contained in it.
+
+    '''
+
+    def __init__(self, gitdir, ref=None):
+        self.gitdir = gitdir
+        self.ref = ref
+
+    def read_morphology(self, name):
+        '''Return the un-parsed text of a morphology.
+        
+        For the given morphology name, locate and return the contents
+        of the morphology as a string.
+
+        Also returns a string describing where in the repository the
+        morphology is located.
+
+        Parsing of this morphology into a form useful for manipulating
+        is handled by the MorphologyLoader class.
+        
+        '''
+        filename = '%s.morph' % name
+        return self.gitdir.read_file(filename, self.ref), filename
+
+    def list_morphologies(self):
+        '''Return the names of all morphologies in the (repo, ref).
+
+        Finds all morphologies in the git directory at the specified
+        ref. Morphology names are returned instead of filenames,
+        so the implementation may change how morphologies are stored
+        in git repositories.
+
+        '''
+
+        def is_morphology_path(path):
+            return path.endswith('.morph')
+
+        def transform_path_to_name(path):
+            return path[:-len('.morph')]
+
+        return (transform_path_to_name(path)
+                for path in self.gitdir.list_files(self.ref)
+                if is_morphology_path(path))
diff --git a/morphlib/morphologyfinder_tests.py b/morphlib/morphologyfinder_tests.py
new file mode 100644
index 00000000..ff83ccff
--- /dev/null
+++ b/morphlib/morphologyfinder_tests.py
@@ -0,0 +1,111 @@
+# Copyright (C) 2013  Codethink Limited
+#
+# 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 of the License.
+#
+# 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
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# =*= License: GPL-2 =*=
+
+
+import os
+import shutil
+import tempfile
+import unittest
+
+import morphlib
+
+
+class MorphologyFinderTests(unittest.TestCase):
+
+    def setUp(self):
+        self.tempdir = tempfile.mkdtemp()
+        self.dirname = os.path.join(self.tempdir, 'repo')
+        os.mkdir(self.dirname)
+        gd = morphlib.gitdir.init(self.dirname)
+        for fn in ('foo', 'bar.morph', 'baz.morph', 'quux'):
+            with open(os.path.join(self.dirname, fn), "w") as f:
+                f.write('dummy morphology text')
+        gd._runcmd(['git', 'add', '.'])
+        gd._runcmd(['git', 'commit', '-m', 'Initial commit'])
+
+        # Changes for difference between commited and work tree
+        newmorphpath = os.path.join(self.dirname, 'foo.morph')
+        os.unlink(os.path.join(self.dirname, 'foo'))
+        with open(newmorphpath, 'w') as f:
+            f.write("altered morphology text")
+
+        # Changes for bare repository
+        self.mirror = os.path.join(self.tempdir, 'mirror')
+        gd._runcmd(['git', 'clone', '--mirror', self.dirname, self.mirror])
+
+    def tearDown(self):
+        shutil.rmtree(self.tempdir)
+
+    def test_list_morphs_in_HEAD(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd, 'HEAD')
+        self.assertEqual(sorted(mf.list_morphologies()),
+                         ['bar', 'baz'])
+
+    def test_list_morphs_in_master(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd, 'master')
+        self.assertEqual(sorted(mf.list_morphologies()),
+                         ['bar', 'baz'])
+
+    def test_list_morphs_raises_with_invalid_ref(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd, 'invalid_ref')
+        self.assertRaises(morphlib.gitdir.InvalidRefError,
+                          mf.list_morphologies)
+
+    def test_list_morphs_in_work_tree(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd)
+        self.assertEqual(sorted(mf.list_morphologies()),
+                         ['bar', 'baz', 'foo'])
+
+    def test_list_morphs_raises_no_worktree_no_ref(self):
+        gd = morphlib.gitdir.GitDirectory(self.mirror)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd)
+        self.assertRaises(morphlib.gitdir.NoWorkingTreeError,
+                          mf.list_morphologies)
+
+    def test_read_morph_in_HEAD(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd, 'HEAD')
+        self.assertEqual(mf.read_morphology('bar')[0],
+                         "dummy morphology text")
+
+    def test_read_morph_in_master(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd, 'master')
+        self.assertEqual(mf.read_morphology('bar')[0],
+                         "dummy morphology text")
+
+    def test_read_morph_raises_with_invalid_ref(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd, 'invalid_ref')
+        self.assertRaises(morphlib.gitdir.InvalidRefError,
+                          mf.read_morphology, 'bar')
+
+    def test_read_morph_in_work_tree(self):
+        gd = morphlib.gitdir.GitDirectory(self.dirname)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd)
+        self.assertEqual(mf.read_morphology('foo')[0],
+                         "altered morphology text")
+
+    def test_read_morph_raises_no_worktree_no_ref(self):
+        gd = morphlib.gitdir.GitDirectory(self.mirror)
+        mf = morphlib.morphologyfinder.MorphologyFinder(gd)
+        self.assertRaises(morphlib.gitdir.NoWorkingTreeError,
+                          mf.read_morphology, 'bar')
diff --git a/morphlib/morphset.py b/morphlib/morphset.py
index 98a4b8f9..c256760e 100644
--- a/morphlib/morphset.py
+++ b/morphlib/morphset.py
@@ -135,18 +135,19 @@ class MorphologySet(object):
                     spec['ref'] == orig_ref and
                     spec['morph'] + '.morph' == morph_filename)
 
-        def change_specs(specs):
+        def change_specs(specs, m):
             for spec in specs:
                 if wanted_spec(spec):
+                    spec['unpetrify-ref'] = spec['ref']
                     spec['ref'] = new_ref
                     m.dirty = True
 
         def change(m):
             if m['kind'] == 'system':
-                change_specs(m['strata'])
+                change_specs(m['strata'], m)
             elif m['kind'] == 'stratum':
-                change_specs(m['chunks'])
-                change_specs(m['build-depends'])
+                change_specs(m['chunks'], m)
+                change_specs(m['build-depends'], m)
 
         for m in self.morphologies:
             change(m)
diff --git a/morphlib/morphset_tests.py b/morphlib/morphset_tests.py
index 7dbc861a..65fe2058 100644
--- a/morphlib/morphset_tests.py
+++ b/morphlib/morphset_tests.py
@@ -127,7 +127,8 @@ class MorphologySetTests(unittest.TestCase):
             {
                 'repo': 'test:morphs',
                 'ref': 'new-ref',
-                'morph': 'foo-stratum'
+                'morph': 'foo-stratum',
+                'unpetrify-ref': 'master',
             })
 
     def test_changes_stratum_ref_in_build_depends(self):
@@ -140,6 +141,7 @@ class MorphologySetTests(unittest.TestCase):
                     'repo': self.stratum.repo_url,
                     'ref': self.stratum.ref,
                     'morph': self.stratum['name'],
+                    'unpetrify-ref': 'master',
                 },
             ]
         })
@@ -157,7 +159,8 @@ class MorphologySetTests(unittest.TestCase):
             {
                 'repo': 'test:morphs',
                 'ref': 'new-ref',
-                'morph': 'foo-stratum'
+                'morph': 'foo-stratum',
+                'unpetrify-ref': 'master',
             })
 
     def test_changes_chunk_ref(self):
@@ -175,6 +178,7 @@ class MorphologySetTests(unittest.TestCase):
                     'repo': 'test:foo-chunk',
                     'ref': 'new-ref',
                     'morph': 'foo-chunk',
+                    'unpetrify-ref': 'master',
                 }
             ])
 
diff --git a/morphlib/plugins/branch_and_merge_new_plugin.py b/morphlib/plugins/branch_and_merge_new_plugin.py
index 61cd40c0..66231de9 100644
--- a/morphlib/plugins/branch_and_merge_new_plugin.py
+++ b/morphlib/plugins/branch_and_merge_new_plugin.py
@@ -44,6 +44,10 @@ class SimpleBranchAndMergePlugin(cliapp.Plugin):
         self.app.add_subcommand(
             'edit', self.edit, arg_synopsis='SYSTEM STRATUM [CHUNK]')
         self.app.add_subcommand(
+            'petrify', self.petrify, arg_synopsis='')
+        self.app.add_subcommand(
+            'unpetrify', self.unpetrify, arg_synopsis='')
+        self.app.add_subcommand(
             'show-system-branch', self.show_system_branch, arg_synopsis='')
         self.app.add_subcommand(
             'show-branch-root', self.show_branch_root, arg_synopsis='')
@@ -604,3 +608,136 @@ class SimpleBranchAndMergePlugin(cliapp.Plugin):
                     % (repo, pretty_command))
             self.app.output.write('\n')
             self.app.output.flush()
+
+    def _load_all_sysbranch_morphologies(self, sb, loader):
+        '''Read in all the morphologies in the root repository.'''
+        self.app.status(msg='Loading in all morphologies')
+        morphs = morphlib.morphset.MorphologySet()
+        mf = morphlib.morphologyfinder.MorphologyFinder(
+            morphlib.gitdir.GitDirectory(
+                sb.get_git_directory_name(sb.root_repository_url)))
+        for morph in mf.list_morphologies():
+            text, filename = mf.read_morphology(morph)
+            m = loader.load_from_string(text, filename=filename)
+            m.repo_url = sb.root_repository_url
+            m.ref = sb.system_branch_name
+            morphs.add_morphology(m)
+        return morphs
+
+    def petrify(self, args):
+        '''Convert all chunk refs in a system branch to be fixed SHA1s.
+
+        This modifies all git commit references in system and stratum
+        morphologies, in the current system branch, to be fixed SHA
+        commit identifiers, rather than symbolic branch or tag names.
+        This is useful for making sure none of the components in a system
+        branch change accidentally.
+
+        Consider the following scenario:
+
+        * The `master` system branch refers to `gcc` using the
+          `baserock/morph` ref. This is appropriate, since the main line
+          of development should use the latest curated code.
+
+        * You create a system branch to prepare for a release, called
+          `TROVE_ID/release/2.0`. The reference to `gcc` is still
+          `baserock/morph`.
+
+        * You test everything, and make a release. You deploy the release
+          images onto devices, which get shipped to your customers.
+
+        * A new version GCC is committed to the `baserock/morph` branch.
+
+        * Your release branch suddenly uses a new compiler, which may
+          or may not work for your particular system at that release.
+
+        To avoid this, you need to _petrify_ all git references
+        so that they do not change accidentally. If you've tested
+        your release with the GCC release that is stored in commit
+        `94c50665324a7aeb32f3096393ec54b2e63bfb28`, then you should
+        continue to use that version of GCC, regardless of what might
+        happen in the master system branch. If, and only if, you decide
+        that a new compiler would be good for your release should you
+        include it in your release branch. This way, only the things
+        that you change intentionally change in your release branch.
+
+        '''
+
+        if args:
+            raise cliapp.AppException('morph petrify takes no arguments')
+
+        ws = morphlib.workspace.open('.')
+        sb = morphlib.sysbranchdir.open_from_within('.')
+        loader = morphlib.morphloader.MorphologyLoader()
+        lrc, rrc = morphlib.util.new_repo_caches(self.app)
+        update_repos = not self.app.settings['no-git-update']
+        done = set()
+
+        morphs = self._load_all_sysbranch_morphologies(sb, loader)
+
+        # Petrify the ref to each stratum and chunk.
+        def petrify_specs(specs):
+            for spec in specs:
+                ref = spec['ref']
+                # Do not double petrify refs
+                if morphlib.git.is_valid_sha1(ref):
+                    continue
+                commit_sha1, tree_sha1 = self.app.resolve_ref(
+                    lrc, rrc, spec['repo'], ref, update=update_repos)
+                assert 'name' in spec or 'morph' in spec
+                filename = '%s.morph' % spec.get('morph', spec.get('name'))
+                morphs.change_ref(spec['repo'], ref, filename, commit_sha1)
+
+        for m in morphs.morphologies:
+            if m['kind'] == 'system':
+                petrify_specs(m['strata'])
+            elif m['kind'] == 'stratum':
+                petrify_specs(m['build-depends'])
+                petrify_specs(m['chunks'])
+
+        # Write morphologies back out again.
+        self._save_dirty_morphologies(loader, sb, morphs.morphologies)
+
+    def unpetrify(self, args):
+        '''Reverse the process of petrification.
+
+        This undoes the changes `morph petrify` did.
+
+        '''
+
+        if args:
+            raise cliapp.AppException('morph petrify takes no arguments')
+
+        ws = morphlib.workspace.open('.')
+        sb = morphlib.sysbranchdir.open_from_within('.')
+        loader = morphlib.morphloader.MorphologyLoader()
+        lrc, rrc = morphlib.util.new_repo_caches(self.app)
+        update_repos = not self.app.settings['no-git-update']
+        done = set()
+
+        morphs = self._load_all_sysbranch_morphologies(sb, loader)
+
+        # Restore the ref for each stratum and chunk
+        def unpetrify_specs(specs):
+            dirty = False
+            for spec in specs:
+                ref = spec['ref']
+                # Don't attempt to unpetrify refs which aren't petrified
+                if not ('unpetrify-ref' in spec
+                        and morphlib.git.is_valid_sha1(ref)):
+                    continue
+                spec['ref'] = spec.pop('unpetrify-ref')
+                dirty = True
+            return dirty
+
+        for m in morphs.morphologies:
+            dirty = False
+            if m['kind'] == 'system':
+                dirty = dirty or unpetrify_specs(m['strata'])
+            elif m['kind'] == 'stratum':
+                dirty = dirty or unpetrify_specs(m['build-depends'])
+                dirty = dirty or unpetrify_specs(m['chunks'])
+            m.dirty = True
+
+        # Write morphologies back out again.
+        self._save_dirty_morphologies(loader, sb, morphs.morphologies)
diff --git a/morphlib/plugins/branch_and_merge_plugin.py b/morphlib/plugins/branch_and_merge_plugin.py
index c1549a5d..671071b6 100644
--- a/morphlib/plugins/branch_and_merge_plugin.py
+++ b/morphlib/plugins/branch_and_merge_plugin.py
@@ -61,8 +61,8 @@ class BranchAndMergePlugin(cliapp.Plugin):
                                 arg_synopsis='BRANCH')
 #        self.app.add_subcommand('edit', self.edit,
 #                                arg_synopsis='SYSTEM STRATUM [CHUNK]')
-        self.app.add_subcommand('petrify', self.petrify)
-        self.app.add_subcommand('unpetrify', self.unpetrify)
+        self.app.add_subcommand('old-petrify', self.petrify)
+        self.app.add_subcommand('old-unpetrify', self.unpetrify)
         self.app.add_subcommand(
             'tag', self.tag, arg_synopsis='TAG-NAME -- [GIT-COMMIT-ARG...]')
         self.app.add_subcommand('build', self.build,
diff --git a/morphlib/sysbranchdir.py b/morphlib/sysbranchdir.py
index 9ad1e2fd..0b3c859a 100644
--- a/morphlib/sysbranchdir.py
+++ b/morphlib/sysbranchdir.py
@@ -95,8 +95,7 @@ class SystemBranchDirectory(object):
 
         # Remove anyleading slashes, or os.path.join below will only
         # use the relative part (since it's absolute, not relative).
-        while relative.startswith('/'):
-            relative = relative[1:]
+        relative = relative.lstrip('/')
 
         return os.path.join(self.root_directory, relative)
 
diff --git a/tests.branching/edit-updates-stratum-build-depends.stdout b/tests.branching/edit-updates-stratum-build-depends.stdout
index 00b303bd..1c6eb8e3 100644
--- a/tests.branching/edit-updates-stratum-build-depends.stdout
+++ b/tests.branching/edit-updates-stratum-build-depends.stdout
@@ -1,46 +1,50 @@
 diff --git a/hello-stratum.morph b/hello-stratum.morph
-index 73ed482..3731d63 100644
+index 73ed482..475fe0f 100644
 --- a/hello-stratum.morph
 +++ b/hello-stratum.morph
-@@ -2,7 +2,7 @@ chunks:
+@@ -2,7 +2,8 @@ chunks:
  - build-depends: []
    build-mode: test
    name: hello
 -  ref: master
 +  ref: newbranch
    repo: test:hello
++  unpetrify-ref: master
  kind: stratum
  name: hello-stratum
 diff --git a/hello-system.morph b/hello-system.morph
-index 721473c..94c1837 100644
+index 721473c..1537f53 100644
 --- a/hello-system.morph
 +++ b/hello-system.morph
-@@ -3,9 +3,8 @@ kind: system
+@@ -3,9 +3,9 @@ kind: system
  name: hello-system
  strata:
  - morph: hello-stratum
 -  ref: master
 +  ref: newbranch
    repo: test:morphs
++  unpetrify-ref: master
  - morph: xyzzy-stratum
    ref: master
    repo: test:morphs
 -system-kind: rootfs-tarball
 diff --git a/xyzzy-stratum.morph b/xyzzy-stratum.morph
-index e302037..97f7208 100644
+index e302037..bcf5b57 100644
 --- a/xyzzy-stratum.morph
 +++ b/xyzzy-stratum.morph
-@@ -1,11 +1,11 @@
+@@ -1,11 +1,13 @@
  build-depends:
  - morph: hello-stratum
 -  ref: master
 +  ref: newbranch
    repo: test:morphs
++  unpetrify-ref: master
  chunks:
  - build-depends: []
    name: hello
 -  ref: master
 +  ref: newbranch
    repo: test:hello
++  unpetrify-ref: master
  kind: stratum
  name: xyzzy-stratum
diff --git a/tests.branching/edit-updates-stratum.stdout b/tests.branching/edit-updates-stratum.stdout
index e84dbe09..32eb820d 100644
--- a/tests.branching/edit-updates-stratum.stdout
+++ b/tests.branching/edit-updates-stratum.stdout
@@ -1,21 +1,22 @@
 diff --git a/hello-stratum.morph b/hello-stratum.morph
-index 73ed482..3731d63 100644
+index 73ed482..475fe0f 100644
 --- a/hello-stratum.morph
 +++ b/hello-stratum.morph
-@@ -2,7 +2,7 @@ chunks:
+@@ -2,7 +2,8 @@ chunks:
  - build-depends: []
    build-mode: test
    name: hello
 -  ref: master
 +  ref: newbranch
    repo: test:hello
++  unpetrify-ref: master
  kind: stratum
  name: hello-stratum
 diff --git a/hello-system.morph b/hello-system.morph
-index b0fed3b..801a955 100644
+index b0fed3b..199c924 100644
 --- a/hello-system.morph
 +++ b/hello-system.morph
-@@ -3,6 +3,5 @@ kind: system
+@@ -3,6 +3,6 @@ kind: system
  name: hello-system
  strata:
  - morph: hello-stratum
@@ -23,3 +24,4 @@ index b0fed3b..801a955 100644
 +  ref: newbranch
    repo: test:morphs
 -system-kind: rootfs-tarball
++  unpetrify-ref: master
diff --git a/tests.branching/workflow.stdout b/tests.branching/workflow.stdout
new file mode 100644
index 00000000..65985486
--- /dev/null
+++ b/tests.branching/workflow.stdout
@@ -0,0 +1 @@
+WARNING: chunk "hello-system.hello-stratum.hello" is now petrified