Revert "Merge branch 'jonathan/fix-petrify'"

This reverts commit cc04afc00f35dc00e03c9ab207bbc2e5513812d0, reversing
changes made to 656295846bffb4eda9fa3869d04fd7c042b2e37a.

1 files changed, 49 insertions, 2 deletions

diff --git a/morphlib/plugins/branch_and_merge_plugin.py b/morphlib/plugins/branch_and_merge_plugin.py
index 2d6b715c..f7109bcf 100644
--- a/morphlib/plugins/branch_and_merge_plugin.py
+++ b/morphlib/plugins/branch_and_merge_plugin.py
@@ -925,13 +925,60 @@ class BranchAndMergePlugin(cliapp.Plugin):
         if len(args) != 0:
             raise cliapp.AppException('morph petrify takes no arguments')
 
+        workspace = self.deduce_workspace()
         branch, branch_path = self.deduce_system_branch()
         root_repo = self.get_branch_config(branch_path, 'branch.root')
         root_repo_dir = self.find_repository(branch_path, root_repo)
         self.lrc, self.rrc = morphlib.util.new_repo_caches(self.app)
 
-        self.petrify_everything(branch, branch_path, root_repo, root_repo_dir,
-                                branch)
+        # We must first get the full set of strata. One same stratum may be
+        # in multiple systems and each system may use a different ref.
+        strata = {}
+        for f in sorted(glob.iglob(os.path.join(root_repo_dir, '*.morph'))):
+            name = os.path.basename(f)[:-len('.morph')]
+            morphology = self.load_morphology(root_repo_dir, name)
+            if morphology['kind'] != 'system':
+                continue
+
+            for stratum_info in morphology['strata']:
+                key = (stratum_info['repo'], stratum_info['morph'])
+                if key in strata:
+                    original_ref = strata[key]
+                    if stratum_info['ref'] == branch:
+                        strata[key] = branch
+                    elif stratum_info['ref'] != original_ref:
+                        if original_ref != branch:
+                            self.app.output.write(
+                                'WARNING: not merging any differences from '
+                                'ref %s into %s of stratum %s\n' %
+                                (stratum_info['ref'], original_ref,
+                                 stratum_info['morph']))
+                        stratum_info['ref'] = branch
+                else:
+                    strata[key] = stratum_info['ref']
+                    stratum_info['ref'] = branch
+            self.update_morphology(root_repo_dir, name, morphology)
+
+        for (repo, morph), ref in strata.iteritems():
+            repo_dir = self.make_available(
+                { 'repo': repo, 'ref': ref, 'morph': morph},
+                branch, branch_path, root_repo, root_repo_dir)
+
+            stratum = self.load_morphology(repo_dir, morph)
+
+            for chunk_info in stratum['chunks']:
+                if (chunk_info['ref'] != branch and
+                        'unpetrify-ref' not in chunk_info):
+                    commit_sha1, tree_sha1 = self.app.resolve_ref(
+                        self.lrc, self.rrc, chunk_info['repo'],
+                        chunk_info['ref'],
+                        update=not self.app.settings['no-git-update'])
+                    chunk_info['unpetrify-ref'] = chunk_info['ref']
+                    chunk_info['ref'] = commit_sha1
+            self.update_morphology(repo_dir, morph, stratum)
+
+        self.print_changelog('The following changes were made but have not '
+                             'been committed')
 
     def unpetrify(self, args):
         '''Reverse the process of petrification'''