Merge remote-tracking branch 'origin/samthursfield/ref-access-fixes'

12 files changed, 257 insertions, 265 deletions

diff --git a/morph b/morph
index f55bce96..0c0789d5 100755
--- a/morph
+++ b/morph
@@ -17,8 +17,5 @@
 
 
 import morphlib
-import os.path
 
-app = morphlib.app.Morph(version=morphlib.__version__)
-app.__file__ = os.path.realpath(__file__)
-app.run()
+morphlib.app.Morph(version=morphlib.__version__).run()
diff --git a/morphlib/cachedrepo.py b/morphlib/cachedrepo.py
index 61526cd7..f0ca627b 100644
--- a/morphlib/cachedrepo.py
+++ b/morphlib/cachedrepo.py
@@ -103,12 +103,6 @@ class CachedRepo(object):
         self.url = url
         self.path = path
 
-    def is_valid_sha1(self, 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])
-
     def resolve_ref(self, ref):
         '''Attempts to resolve a ref into its SHA1 and tree SHA1.
 
@@ -117,7 +111,7 @@ class CachedRepo(object):
 
         '''
 
-        if not self.is_valid_sha1(ref):
+        if not morphlib.git.is_valid_sha1(ref):
             try:
                 refs = self._show_ref(ref).split('\n')
                 refs = [x.split() for x in refs]
@@ -143,7 +137,7 @@ class CachedRepo(object):
 
         '''
 
-        if not self.is_valid_sha1(ref):
+        if not morphlib.git.is_valid_sha1(ref):
             raise UnresolvedNamedReferenceError(self, ref)
         try:
             sha1 = self._rev_list(ref).strip()
@@ -194,6 +188,15 @@ class CachedRepo(object):
 
         self._checkout_ref(ref, target_dir)
 
+    def load_morphology(self, ref, name):
+        '''Loads a morphology from a given ref'''
+
+        if not morphlib.git.is_valid_sha1(ref):
+            ref = self._rev_list(ref).strip()
+        text = self.cat(ref, '%s.morph' % name)
+        morphology = morphlib.morph2.Morphology(text)
+        return morphology
+
     def ls_tree(self, ref):
         '''Return file names found in root tree. Does not recurse to subtrees.
 
@@ -203,7 +206,7 @@ class CachedRepo(object):
 
         '''
 
-        if not self.is_valid_sha1(ref):
+        if not morphlib.git.is_valid_sha1(ref):
             raise UnresolvedNamedReferenceError(self, ref)
         try:
             sha1 = self._rev_list(ref).strip()
diff --git a/morphlib/cachedrepo_tests.py b/morphlib/cachedrepo_tests.py
index 0a87b32a..0ca0882f 100644
--- a/morphlib/cachedrepo_tests.py
+++ b/morphlib/cachedrepo_tests.py
@@ -26,6 +26,11 @@ from morphlib import cachedrepo
 
 class CachedRepoTests(unittest.TestCase):
 
+    EXAMPLE_MORPH = '''{
+        "name": "foo",
+        "kind": "chunk"
+    }'''
+
     def show_ref(self, ref):
         output = {
             'master':
@@ -57,6 +62,7 @@ class CachedRepoTests(unittest.TestCase):
 
     def rev_list(self, ref):
         output = {
+            'master': 'e28a23812eadf2fce6583b8819b9c5dbd36b9fb9',
             'e28a23812eadf2fce6583b8819b9c5dbd36b9fb9':
             'e28a23812eadf2fce6583b8819b9c5dbd36b9fb9',
             'a4da32f5a81c8bc6d660404724cedc3bc0914a75':
@@ -70,7 +76,7 @@ class CachedRepoTests(unittest.TestCase):
     def cat_file(self, ref, filename):
         output = {
             'e28a23812eadf2fce6583b8819b9c5dbd36b9fb9:foo.morph':
-            'contents of foo.morph'
+            self.EXAMPLE_MORPH
         }
         try:
             return output['%s:%s' % (ref, filename)]
@@ -165,7 +171,7 @@ class CachedRepoTests(unittest.TestCase):
     def test_cat_existing_file_in_existing_ref(self):
         data = self.repo.cat('e28a23812eadf2fce6583b8819b9c5dbd36b9fb9',
                              'foo.morph')
-        self.assertEqual(data, 'contents of foo.morph')
+        self.assertEqual(data, self.EXAMPLE_MORPH)
 
     def test_fail_cat_file_in_invalid_ref(self):
         self.assertRaises(cachedrepo.InvalidReferenceError, self.repo.cat,
@@ -216,6 +222,10 @@ class CachedRepoTests(unittest.TestCase):
         morph_filename = os.path.join(unpack_dir, 'foo.morph')
         self.assertTrue(os.path.exists(morph_filename))
 
+    def test_load_morphology_from_existing_ref(self):
+        morph = self.repo.load_morphology('master', 'foo')
+        self.assertTrue(morph['name'] == 'foo')
+
     def test_ls_tree_in_existing_ref(self):
         data = self.repo.ls_tree('e28a23812eadf2fce6583b8819b9c5dbd36b9fb9')
         self.assertEqual(data, ['foo.morph'])
diff --git a/morphlib/git.py b/morphlib/git.py
index 5862ef9b..b3dd2c45 100644
--- a/morphlib/git.py
+++ b/morphlib/git.py
@@ -221,7 +221,12 @@ def clone_into(runcmd, srcpath, targetpath, ref=None):
     else:
         runcmd(['git', 'clone', '-b', ref, srcpath, targetpath])
 
-def find_first_ref(runcmd, gitdir, ref):
-    '''Find the *first* ref match and returns its sha1.'''
-    return runcmd(['git', 'show-ref', ref],
-                  cwd=gitdir).split("\n")[0].split(" ")[0]
+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])
+
+def rev_parse(runcmd, gitdir, ref):
+    '''Find the sha1 for the given ref'''
+    return runcmd(['git', 'rev-parse', ref], cwd=gitdir)[0:40]
diff --git a/morphlib/plugins/branch_and_merge_plugin.py b/morphlib/plugins/branch_and_merge_plugin.py
index 279a9948..a3faa0c2 100644
--- a/morphlib/plugins/branch_and_merge_plugin.py
+++ b/morphlib/plugins/branch_and_merge_plugin.py
@@ -57,8 +57,6 @@ class BranchAndMergePlugin(cliapp.Plugin):
                                 arg_synopsis='SYSTEM')
         self.app.add_subcommand('foreach', self.foreach,
                                 arg_synopsis='COMMAND')
-        # This command should be hidden, once cliapp supports such a thing
-        self.app.add_subcommand('merge-morphology', self.merge_morphology)
 
     def disable(self):
         pass
@@ -160,6 +158,20 @@ class BranchAndMergePlugin(cliapp.Plugin):
                 changes.append(paths.split()[0])
         return changes
 
+    def get_unmerged_changes(self, repo_dir, env={}):
+        '''Identifies files which have unresolved merge conflicts'''
+
+        # The second column of the git command output is set either if the
+        # file has changes in the working tree or if it has conflicts.
+        status = self.app.runcmd(['git', 'status', '--porcelain'],
+                                 cwd=repo_dir, env=env)
+        changes = []
+        for change in status.strip().splitlines():
+            xy, paths = change[0:2], change[2:].strip()
+            if xy[1] != ' ' and xy != '??':
+                changes.append(paths.split()[0])
+        return changes
+
     def resolve_ref(self, repodir, ref):
         try:
             return self.app.runcmd(['git', 'show-ref', ref],
@@ -174,6 +186,21 @@ class BranchAndMergePlugin(cliapp.Plugin):
             self.app.settings['repo-alias'])
         return resolver.pull_url(reponame)
 
+    def get_cached_repo(self, repo_name):
+        '''Return CachedRepo object from the local repository cache
+
+        Repo is cached and updated if necessary. The cache itself has a
+        mechanism in place to avoid multiple updates per Morph invocation.
+        '''
+
+        self.app.status(msg='Updating git repository %s in cache' % repo_name)
+        if not self.app.settings['no-git-update']:
+            repo = self.lrc.cache_repo(repo_name)
+            repo.update()
+        else:
+            repo = self.lrc.get_repo(repo_name)
+        return repo
+
     def clone_to_directory(self, dirname, reponame, ref):
         '''Clone a repository below a directory.
 
@@ -182,16 +209,9 @@ class BranchAndMergePlugin(cliapp.Plugin):
         '''
 
         # Setup.
-        cache = morphlib.util.new_repo_caches(self.app)[0]
         resolver = morphlib.repoaliasresolver.RepoAliasResolver(
             self.app.settings['repo-alias'])
-
-        # Get the repository into the cache; make sure it is up to date.
-        self.app.status(msg='Updating git repository %(reponame)s in cache',
-                        reponame=reponame)
-        repo = cache.cache_repo(reponame)
-        if not self.app.settings['no-git-update']:
-            repo.update()
+        repo = self.get_cached_repo(reponame)
 
         # Make sure the parent directories needed for the repo dir exist.
         parent_dir = os.path.dirname(dirname)
@@ -221,12 +241,22 @@ class BranchAndMergePlugin(cliapp.Plugin):
         self.app.runcmd(['git', 'remote', 'update'], cwd=dirname)
 
     def load_morphology(self, repo_dir, name, ref=None):
+        '''Loads a morphology from a repo in a system branch
+
+        If 'ref' is specified, the version is taken from there instead of the
+        working tree. Note that you shouldn't use this to fetch files on
+        branches other than the current system branch, because the remote in
+        the system branch repo may be completely out of date. Use the local
+        repository cache instead for this.
+        '''
+
         if ref is None:
             filename = os.path.join(repo_dir, '%s.morph' % name)
             with open(filename) as f:
                 text = f.read()
         else:
-            ref = morphlib.git.find_first_ref(self.app.runcmd, repo_dir, ref)
+            if not morphlib.git.is_valid_sha1(ref):
+                ref = morphlib.git.rev_parse(self.app.runcmd, repo_dir, ref)
             try:
                 text = self.app.runcmd(['git', 'cat-file', 'blob',
                                        '%s:%s.morph' % (ref, name)],
@@ -389,6 +419,7 @@ class BranchAndMergePlugin(cliapp.Plugin):
         workspace = self.deduce_workspace()
         branch_dir = os.path.join(workspace, new_branch)
         os.makedirs(branch_dir)
+        self.lrc, self.rrc = morphlib.util.new_repo_caches(self.app)
 
         try:
             # Create a .morph-system-branch directory to clearly identify
@@ -434,6 +465,7 @@ class BranchAndMergePlugin(cliapp.Plugin):
         workspace = self.deduce_workspace()
         branch_dir = os.path.join(workspace, system_branch)
         os.makedirs(branch_dir)
+        self.lrc, self.rrc = morphlib.util.new_repo_caches(self.app)
 
         try:
             # Create a .morph-system-branch directory to clearly identify
@@ -504,30 +536,29 @@ class BranchAndMergePlugin(cliapp.Plugin):
                                       (' '.join(command), repo, error))
         return repo_dir
 
-    def edit_stratum(self, system_branch, branch_dir, branch_root_dir,
-                     stratum):
-        # Make the stratum repository and the ref available locally.
-        stratum_repo_dir = self.checkout_repository(
-            branch_dir, stratum['repo'], system_branch,
-            parent_ref=stratum['ref'])
-
-        # Check if we need to change anything at all.
-        if stratum['ref'] != system_branch:
-            # If the stratum is in the same repository as the system,
-            # copy its morphology from its source ref into the system branch.
-            if branch_root_dir == stratum_repo_dir:
-                stratum_morphology = self.load_morphology(
-                    branch_root_dir, stratum['morph'], ref=stratum['ref'])
-                self.save_morphology(
-                    branch_root_dir, stratum['morph'], stratum_morphology)
+    def edit_stratum(self, system_branch, branch_dir, branch_root,
+                     branch_root_dir, stratum):
+        if stratum['repo'] == branch_root:
+            stratum_repo_dir = branch_root_dir
+            if stratum['ref'] != system_branch:
+                # We need to bring the morphology forwards from its ref to the
+                # current HEAD
+                repo = self.lrc.get_repo(branch_root)
+                stratum_morphology = repo.load_morphology(
+                    stratum['ref'], stratum['morph'])
+                self.save_morphology(branch_root_dir,
+                    stratum['morph'], stratum_morphology)
                 self.log_change(
                     stratum['repo'],
                     '"%s" copied from "%s" to "%s"' %
                     (stratum['morph'], stratum['ref'], system_branch))
+        else:
+            # Make sure the stratum repository is available
+            stratum_repo_dir = self.checkout_repository(
+                branch_dir, stratum['repo'], system_branch,
+                parent_ref=stratum['ref'])
 
-            # Update the reference to the stratum in the system morphology.
-            stratum['ref'] = system_branch
-
+        stratum['ref'] = system_branch
         return stratum_repo_dir
 
     def edit_chunk(self, system_branch, branch_dir, stratum_repo_dir, chunk):
@@ -564,13 +595,15 @@ class BranchAndMergePlugin(cliapp.Plugin):
         stratum_name = args[1]
         chunk_name = args[2] if len(args) > 2 else None
 
+        self.lrc, self.rrc = morphlib.util.new_repo_caches(self.app)
+
         # Load the system morphology and find out which repo and ref
         # we need to edit the stratum.
         system_morphology = self.load_morphology(branch_root_dir, system_name)
         stratum = self.get_edit_info(system_name, system_morphology,
                                      stratum_name, collection='strata')
         stratum_repo_dir = self.edit_stratum(
-            system_branch, branch_dir, branch_root_dir, stratum)
+            system_branch, branch_dir, branch_root, branch_root_dir, stratum)
         self.save_morphology(branch_root_dir, system_name,
                              system_morphology)
         self.log_change(branch_root,
@@ -615,7 +648,7 @@ class BranchAndMergePlugin(cliapp.Plugin):
         root_repo = self.get_branch_config(branch_path, 'branch.root')
         root_repo_dir = self.find_repository(branch_path, root_repo)
 
-        lrc, rrc = morphlib.util.new_repo_caches(self.app)
+        self.lrc, self.rrc = morphlib.util.new_repo_caches(self.app)
 
         for f in glob.glob(os.path.join(root_repo_dir, '*.morph')):
             name = os.path.basename(f)[:-len('.morph')]
@@ -625,14 +658,16 @@ class BranchAndMergePlugin(cliapp.Plugin):
 
             for stratum_info in morphology['strata']:
                 repo_dir = self.edit_stratum(
-                    branch, branch_path, root_repo_dir, stratum_info)
+                    branch, branch_path, root_repo, root_repo_dir,
+                    stratum_info)
 
                 stratum = self.load_morphology(repo_dir, stratum_info['morph'])
 
                 for chunk_info in stratum['chunks']:
                     if 'unpetrify-ref' not in chunk_info:
                         commit_sha1, tree_sha1 = self.app.resolve_ref(
-                            lrc, rrc, chunk_info['repo'], chunk_info['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
@@ -658,6 +693,8 @@ class BranchAndMergePlugin(cliapp.Plugin):
         if len(args) != 0:
             raise cliapp.AppException('morph unpetrify takes no arguments')
 
+        self.lrc, self.rrc = morphlib.util.new_repo_caches(self.app)
+
         workspace = self.deduce_workspace()
         branch, branch_path = self.deduce_system_branch()
         root_repo = self.get_branch_config(branch_path, 'branch.root')
@@ -671,7 +708,8 @@ class BranchAndMergePlugin(cliapp.Plugin):
 
             for stratum_info in morphology['strata']:
                 repo_dir = self.edit_stratum(
-                    branch, branch_path, root_repo_dir, stratum_info)
+                    branch, branch_path, root_repo, root_repo_dir,
+                    stratum_info)
 
                 stratum = self.load_morphology(repo_dir, stratum_info['morph'])
 
@@ -686,46 +724,16 @@ class BranchAndMergePlugin(cliapp.Plugin):
         self.print_changelog('The following changes were made but have not '
                              'been comitted')
 
-    def load_morphology_pair(self, repo_dir, ref, name):
-        '''Load two versions of a morphology and check for major conflicts
-
-        Returns the version at 'ref' (if it exists) and the on-disk version.
+    # When 'merge' is unset, git doesn't try to resolve conflicts itself in
+    # those files.
+    MERGE_ATTRIBUTE = '*.morph\t-merge\n'
 
-        '''
-
-        new = self.load_morphology(repo_dir, name)
-        try:
-            old = self.load_morphology(repo_dir, name, ref=ref)
-        except cliapp.AppException as e:
-            return None, new
-
-        if old['name'] != new['name']:
-            # We should enforce this in validation during load_morphology()
-            # rather than having to check it here
-            raise cliapp.AppException(
-                'merge confict: "name" of morphology %s (name should '
-                'always match filename)' % name)
-        if old['kind'] != new['kind']:
-            raise cliapp.AppException(
-                'merge conflict: "kind" of morphology %s' % name)
-
-        return old, new
-
-    def configure_merge_driver(self, repo_dir):
-        self.set_repo_config(repo_dir, 'merge.morph.name',
-            'Morphology merge driver')
-        self.set_repo_config(repo_dir, 'merge.morph.driver',
-            '%s merge-morphology $MORPH_FROM_BRANCH $MORPH_TO_BRANCH '
-            '%%O %%A %%B' % self.app.__file__)
-
-    MERGE_ATTRIBUTE = '*.morph\tmerge=morph\n'
-
-    def enable_merge_driver(self, repo_dir):
+    def disable_morph_merging(self, repo_dir):
         attributes_file = os.path.join(repo_dir, ".git", "info", "attributes")
         with open(attributes_file, 'a') as f:
             f.write(self.MERGE_ATTRIBUTE)
 
-    def disable_merge_driver(self, repo_dir):
+    def enable_morph_merging(self, repo_dir):
         attributes_file = os.path.join(repo_dir, ".git", "info", "attributes")
         with open(attributes_file, 'r') as f:
             attributes = f.read()
@@ -735,38 +743,46 @@ class BranchAndMergePlugin(cliapp.Plugin):
             with morphlib.savefile.SaveFile(attributes_file, 'w') as f:
                 f.write(attributes[:-len(self.MERGE_ATTRIBUTE)])
 
-    def merge_repo(self, dirty_repos, failed_repos,
-                   from_branch_dir, from_repo, from_ref,
-                   to_branch_dir, to_repo, to_ref):
-        '''Merge changes for a system branch in a specific repository
+    def get_merge_files(self, repo_dir, from_sha1, to_ref, name):
+        '''Returns merge base, remote and local versions of a morphology
+
+        We already ran 'git fetch', so the remote branch is available within
+        the target repository.
+
+        '''
+
+        base_sha1 = self.app.runcmd(['git', 'merge-base', from_sha1, to_ref],
+                                    cwd=repo_dir).strip()
+        base_morph = self.load_morphology(repo_dir, name, ref=base_sha1)
+        from_morph = self.load_morphology(repo_dir, name, ref=from_sha1)
+        to_morph = self.load_morphology(repo_dir, name, ref=to_ref)
 
-        This done using a standard 'git pull', with a custom merge driver to
-        handle the .morph files.
+        if from_morph['name'] != to_morph['name']:
+            # We should enforce name == filename in load_morphology()
+            raise cliapp.AppException(
+                'merge conflict: "name" of morphology %s (name should always '
+                'match filename)' % name)
+        if from_morph['kind'] != to_morph['kind']:
+            raise cliapp.AppException(
+                'merge conflict: "kind" of morphology %s changed from %s to %s'
+                % (name, from_morph['kind'], to_morph['kind']))
+
+        return base_morph, from_morph, to_morph
 
-        The merge driver is only invoked when there is a three-way merge
-        conflict on a file. If the file has changed in the FROM branch but not
-        in the TO branch (relative to the base version) git will choose the
-        FROM version without considering its contents.
+    def merge_repo(self, merged_repos, from_branch_dir, from_repo, from_ref,
+                   to_branch_dir, to_repo, to_ref):
+        '''Merge changes for a system branch in a specific repository
 
-        Since git may automatically update morphologies in TO to use the refs
-        out of FROM, the merge driver does the same, and we then reset them
-        back and write the morphologies out again after recursively merging
-        the components. It's important that we disable the merge driver again
-        after the pull, or we risk confusing later users of the same repo who
-        do a manual git merge.
+        We disable merging for morphologies and do this manually later on.
 
         '''
 
-        if to_repo in failed_repos:
-            return None
+        if to_repo in merged_repos:
+            return merged_repos[to_repo]
 
         from_repo_dir = self.find_repository(from_branch_dir, from_repo)
         to_repo_dir = self.checkout_repository(to_branch_dir, to_repo, to_ref)
 
-        if to_repo_dir in dirty_repos:
-            return to_repo_dir
-        dirty_repos.add(to_repo_dir)
-
         if self.get_uncommitted_changes(from_repo_dir) != []:
             raise cliapp.AppException('repository %s has uncommitted '
                                       'changes' % from_repo)
@@ -774,41 +790,42 @@ class BranchAndMergePlugin(cliapp.Plugin):
             raise cliapp.AppException('repository %s has uncommitted '
                                       'changes' % to_repo)
 
-        self.configure_merge_driver(to_repo_dir)
-        self.enable_merge_driver(to_repo_dir)
-        env = dict(os.environ)
-        env['MORPH_FROM_BRANCH'] = from_ref
-        env['MORPH_TO_BRANCH'] = to_ref
-        # ':' in pathnames confuses git, so we have to pass it a URL
-        from_url = urlparse.urljoin('file://', from_repo_dir)
+        # Fetch the local FROM branch; its sha1 will be stored in FETCH_HEAD.
+        # ':' in pathnames confuses git, so we have to pass it a URL.
+        from_repo_url = urlparse.urljoin('file://', from_repo_dir)
+        self.app.runcmd(['git', 'fetch', from_repo_url, from_ref],
+                        cwd=to_repo_dir)
+
+        # Merge everything but the morphologies; error output is ignored (it's
+        # not very good) and instead we report conflicts manually later on.
+        self.disable_morph_merging(to_repo_dir)
+        with open(os.path.join(to_repo_dir, '.git', 'FETCH_HEAD')) as f:
+            from_sha1 = f.read(40)
         status, output, error = self.app.runcmd_unchecked(
-            ['git', 'pull', '--quiet', '--no-commit', '--no-ff',
-             from_url, from_ref], cwd=to_repo_dir, env=env)
-        self.disable_merge_driver(to_repo_dir)
-
-        if status != 0:
-            self.app.output.write(
-                'Merge errors encountered in %s, branch %s:\n%s'
-                % (to_repo, to_ref, output))
+            ['git', 'merge', '--no-commit', '--no-ff', from_sha1],
+            cwd=to_repo_dir)
+        self.enable_morph_merging(to_repo_dir)
 
-        if status != 0:
-            self.app.output.write('\n')
-            failed_repos.add(to_repo)
-            return None
-        return to_repo_dir
+        merged_repos[to_repo] = (to_repo_dir, from_sha1)
+        return (to_repo_dir, from_sha1)
 
     def merge(self, args):
-        '''Pull and merge changes from a system branch into the current one.'''
+        '''Pull and merge changes from a system branch into the current one.
+
+        The remote branch is pulled from the current workspace into the target
+        repositories (so any local commits are included).
+
+        '''
 
         if len(args) != 1:
             raise cliapp.AppException('morph merge requires a system branch '
                                       'name as its argument')
 
+        self.lrc, self.rrc = morphlib.util.new_repo_caches(self.app)
         workspace = self.deduce_workspace()
         from_branch = args[0]
         from_branch_dir = self.find_system_branch(workspace, from_branch)
         to_branch, to_branch_dir = self.deduce_system_branch()
-
         if from_branch_dir is None:
             raise cliapp.AppException('branch %s must be checked out before '
                                       'it can be merged' % from_branch)
@@ -821,26 +838,22 @@ class BranchAndMergePlugin(cliapp.Plugin):
                                       (root_repo, other_root_repo))
 
         def merge_chunk(old_ci, ci):
-            self.merge_repo(
-                dirty_repo_dirs, failed_repos,
+            self.merge_repo(merged_repos,
                 from_branch_dir, old_ci['repo'], from_branch,
                 to_branch_dir, ci['repo'], ci['ref'])
 
         def merge_stratum(old_si, si):
-            to_repo_dir = self.merge_repo(
-                dirty_repo_dirs, failed_repos,
+            to_repo_dir, from_sha1 = self.merge_repo(merged_repos,
                 from_branch_dir, old_si['repo'], from_branch,
                 to_branch_dir, si['repo'], si['ref'])
-            if to_repo_dir is None:
-                return
+            base_morph, from_morph, to_morph = self.get_merge_files(
+                to_repo_dir, from_sha1, si['ref'], si['morph'])
 
-            old_stratum, stratum = self.load_morphology_pair(
-                to_repo_dir, old_si['ref'], si['morph'])
             changed = False
-            edited_chunks = [ci for ci in stratum['chunks']
+            edited_chunks = [ci for ci in from_morph['chunks']
                              if ci['ref'] == from_branch]
             for ci in edited_chunks:
-                for old_ci in old_stratum['chunks']:
+                for old_ci in to_morph['chunks']:
                     if old_ci['repo'] == ci['repo']:
                         break
                 else:
@@ -852,22 +865,21 @@ class BranchAndMergePlugin(cliapp.Plugin):
                 ci['ref'] = old_ci['ref']
                 merge_chunk(old_ci, ci)
             if changed:
-                self.save_morphology(to_repo_dir, si['morph'], stratum)
+                self.save_morphology(to_repo_dir, si['morph'], to_morph)
                 self.app.runcmd(['git', 'add', si['morph'] + '.morph'],
                                 cwd=to_repo_dir)
 
         def merge_system(name):
-            old_morphology, morphology = self.load_morphology_pair(
-                to_root_dir, to_branch, name)
-
-            if morphology['kind'] != 'system':
+            base_morph, from_morph, to_morph = self.get_merge_files(
+                to_root_dir, from_sha1, to_branch, name)
+            if to_morph['kind'] != 'system':
                 return
 
             changed = False
-            edited_strata = [si for si in morphology['strata']
+            edited_strata = [si for si in from_morph['strata']
                              if si['ref'] == from_branch]
             for si in edited_strata:
-                for old_si in old_morphology['strata']:
+                for old_si in to_morph['strata']:
                     # We make no attempt at rename / move detection
                     if old_si['morph'] == si['morph'] \
                             and old_si['repo'] == si['repo']:
@@ -881,114 +893,45 @@ class BranchAndMergePlugin(cliapp.Plugin):
                 si['ref'] = old_si['ref']
                 merge_stratum(old_si, si)
             if changed:
-                self.save_morphology(to_root_dir, name, morphology)
+                self.save_morphology(to_root_dir, name, to_morph)
                 self.app.runcmd(['git', 'add', f], cwd=to_root_dir)
 
-        dirty_repo_dirs = set()
-        failed_repos = set()
-
+        merged_repos = {}
         try:
-            to_root_dir = self.merge_repo(
-                dirty_repo_dirs, failed_repos,
+            to_root_dir, from_sha1 = self.merge_repo(merged_repos,
                 from_branch_dir, root_repo, from_branch,
                 to_branch_dir, root_repo, to_branch)
-            if to_root_dir is None:
-                raise cliapp.AppException(
-                    'Merging failed in %s: please \'git merge\' the latest %s '
-                    'into %s in the \'%s\' system branch.' %
-                    (root_repo, to_branch, from_branch, from_branch))
 
             for f in glob.glob(os.path.join(to_root_dir, '*.morph')):
                 name = os.path.basename(f)[:-len('.morph')]
                 merge_system(name)
 
-            if len(failed_repos) > 0:
-                raise cliapp.AppException(
-                    'merge errors were encountered in the following %s:\n\n'
-                    '\t%s\n\nPlease manually merge the target ref into %s in '
-                    'each case in the %s system branch, and then repeat the '
-                    'system branch merge.' %
-                    ('repository' if len(failed_repos)==1 else 'repositories',
-                     '\n\t'.join(failed_repos), from_branch, from_branch))
-
-            for repo_dir in dirty_repo_dirs:
-                # Repo will often turn out to not be dirty: if the changes we
-                # merged only updated refs to the system branch, we will have
-                # changed them back again so that the index will now be empty.
-                if morphlib.git.index_has_changes(self.app.runcmd, repo_dir):
+            success = True
+            for repo_name, repo_info in merged_repos.iteritems():
+                repo_dir = repo_info[0]
+                conflicts = self.get_unmerged_changes(repo_dir)
+                if len(conflicts) > 0:
+                    self.app.output.write("Merge conflicts in %s:\n\t%s\n" %
+                        (repo_name, '\n\t'.join(conflicts)))
+                    success = False
+                elif morphlib.git.index_has_changes(self.app.runcmd, repo_dir):
+                    # Repo may not be dirty if the changes only touched refs,
+                    # because they may now match the previous state.
                     msg = "Merge system branch '%s'" % from_branch
                     self.app.runcmd(['git', 'commit', '--all', '-m%s' % msg],
                                     cwd=repo_dir)
-
+            if not success:
+                raise cliapp.AppException(
+                    "merge errors were encountered. Please manually merge the "
+                    "target ref into %s in the remote system branch in each "
+                    "case, and then repeat the 'morph merge' operation." %
+                    from_branch)
             self.app.status(msg="Merge successful")
         except:
-            for repo_dir in dirty_repo_dirs:
+            for repo_dir, sha1 in merged_repos.itervalues():
                 self.reset_work_tree_safe(repo_dir)
             raise
 
-    def merge_morphology_contents(self, from_branch, from_morph, to_morph):
-        if from_morph['kind'] != to_morph['kind'] or \
-           from_morph['name'] != to_morph['name']:
-            raise cliapp.AppException('mismatch in name or kind')
-
-        pairs = []
-        if to_morph['kind'] == 'system':
-            pairs = zip(from_morph['strata'], to_morph['strata'])
-        elif to_morph['kind'] == 'stratum':
-            pairs = zip(from_morph['chunks'], to_morph['chunks'])
-
-        for from_child, to_child in pairs:
-            if from_child['morph'] != to_child['morph'] or \
-               from_child['repo'] != to_child['repo']:
-                continue
-
-            # 'morph merge' has two stages, of which this is the first. In the
-            # second stage we iterate each component whose 'ref' points to
-            # 'from_branch', merge inside its repository, and then update the
-            # morphology again to point at the merged ref in that repository.
-            # That is why we apparently merge the 'ref' field backwards here.
-            if from_child['ref'] == from_branch:
-                to_child['ref'] = from_branch
-
-    def merge_morphology(self, args):
-        '''Automatically merge changes between two conflicting morphologies.
-
-        Normally executed as a git merge driver.
-
-        In the future, this function can be expanded to resolve changes in
-        field ordering.
-
-        '''
-
-        if len(args) != 5:
-            raise cliapp.AppException('this command is not meant to be run '
-                                      'manually.')
-
-        from_branch = args[0]
-        to_branch = args[1]
-        base_file = args[2]
-        to_file = args[3]     # local
-        from_file = args[4]   # remote
-
-        with open(from_file) as f:
-            from_morph = morphlib.morph2.Morphology(f.read())
-        with open(to_file) as f:
-            to_morph = morphlib.morph2.Morphology(f.read())
-
-        self.merge_morphology_contents(from_branch, from_morph, to_morph)
-
-        # git merge gives us temporary files which we can overwrite with our
-        # resolution
-        with morphlib.savefile.SaveFile(to_file, 'w') as f:
-            to_morph.write_to_file(f)
-
-        # Leave the rest of the merging to git for now.
-        status, output, error = self.app.runcmd_unchecked(
-            ['git', 'merge-file', '-LHEAD', '-LBASE', '-L%s' % from_branch,
-             to_file, base_file, from_file])
-        if status != 0:
-            raise cliapp.AppException('Morph did not resolve all conflicts')
-
     def build(self, args):
         if len(args) != 1:
             raise cliapp.AppException('morph build expects exactly one '
diff --git a/tests.branching/ambiguous-refs.script b/tests.branching/ambiguous-refs.script
new file mode 100755
index 00000000..3321a310
--- /dev/null
+++ b/tests.branching/ambiguous-refs.script
@@ -0,0 +1,49 @@
+#!/bin/sh
+# Copyright (C) 2012  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.
+
+
+# 'git show-ref master' sorts its output alphebetically, so we can't rely on
+# it to resolve 'master': we might get 'alpha/master' instead.
+
+set -eu
+
+. "$SRCDIR/scripts/fix-committer-info"
+
+# Disable test on versions of Python before 2.7.
+if ! python --version 2>&1 | grep '^Python 2\.[78]' > /dev/null
+then
+    exit 0
+fi
+
+cd "$DATADIR/morphs"
+git mv hello-stratum.morph goodbye-stratum.morph
+sed -e 's/"morph": "hello-stratum"/"morph": "goodbye-stratum"/' \
+    -i hello-system.morph
+
+git commit --quiet -am "Rename hello-system"
+
+cd "$DATADIR/workspace"
+"$SRCDIR/scripts/test-morph" init
+"$SRCDIR/scripts/test-morph" branch baserock:morphs release
+
+# Create an extra ref to confuse any users of git show-ref
+cd release/baserock:morphs
+git checkout --quiet -b alpha/master HEAD~1
+git checkout --quiet release
+
+# The petrify will fail if we resolved 'master' as 'alpha/master' by mistake.
+cd "$DATADIR/workspace/release/baserock:morphs"
+"$SRCDIR/scripts/test-morph" petrify
diff --git a/tests.branching/merge-conflict-chunks.stderr b/tests.branching/merge-conflict-chunks.stderr
index 9692d2ec..57aafa5a 100644
--- a/tests.branching/merge-conflict-chunks.stderr
+++ b/tests.branching/merge-conflict-chunks.stderr
@@ -1,6 +1 @@
-ERROR: merge errors were encountered in the following repositories:
-
-	baserock:stratum2-hello
-	baserock:stratum3-hello
-
-Please manually merge the target ref into test/feature in each case in the test/feature system branch, and then repeat the system branch merge.
+ERROR: merge errors were encountered. Please manually merge the target ref into test/feature in the remote system branch in each case, and then repeat the 'morph merge' operation.
diff --git a/tests.branching/merge-conflict-chunks.stdout b/tests.branching/merge-conflict-chunks.stdout
index 75d50c7f..bf6d3828 100644
--- a/tests.branching/merge-conflict-chunks.stdout
+++ b/tests.branching/merge-conflict-chunks.stdout
@@ -1,10 +1,4 @@
-Merge errors encountered in baserock:stratum2-hello, branch test/stable:
-Auto-merging conflict.txt
-CONFLICT (add/add): Merge conflict in conflict.txt
-Automatic merge failed; fix conflicts and then commit the result.
-
-Merge errors encountered in baserock:stratum3-hello, branch test/stable:
-Auto-merging conflict.txt
-CONFLICT (add/add): Merge conflict in conflict.txt
-Automatic merge failed; fix conflicts and then commit the result.
-
+Merge conflicts in baserock:stratum2-hello:
+	conflict.txt
+Merge conflicts in baserock:stratum3-hello:
+	conflict.txt
diff --git a/tests.branching/merge-conflict-stratum.stderr b/tests.branching/merge-conflict-stratum.stderr
index 3a7c1522..57aafa5a 100644
--- a/tests.branching/merge-conflict-stratum.stderr
+++ b/tests.branching/merge-conflict-stratum.stderr
@@ -1 +1 @@
-ERROR: Merging failed in baserock:morphs: please 'git merge' the latest test/stable into test/feature in the 'test/feature' system branch.
+ERROR: merge errors were encountered. Please manually merge the target ref into test/feature in the remote system branch in each case, and then repeat the 'morph merge' operation.
diff --git a/tests.branching/merge-conflict-stratum.stdout b/tests.branching/merge-conflict-stratum.stdout
index 20064406..cce0973c 100644
--- a/tests.branching/merge-conflict-stratum.stdout
+++ b/tests.branching/merge-conflict-stratum.stdout
@@ -1,6 +1,2 @@
-Merge errors encountered in baserock:morphs, branch test/stable:
-Auto-merging hello-system.morph
-Auto-merging hello-stratum.morph
-CONFLICT (content): Merge conflict in hello-stratum.morph
-Automatic merge failed; fix conflicts and then commit the result.
-
+Merge conflicts in baserock:morphs:
+	hello-stratum.morph
diff --git a/tests.branching/merge-handles-unmergable-cases.stderr b/tests.branching/merge-handles-unmergable-cases.stderr
index 513db2b8..64c9c34b 100644
--- a/tests.branching/merge-handles-unmergable-cases.stderr
+++ b/tests.branching/merge-handles-unmergable-cases.stderr
@@ -1 +1 @@
-ERROR: merge conflict: "kind" of morphology hello-stratum
+ERROR: merge conflict: "kind" of morphology hello-stratum changed from chunk to stratum
diff --git a/tests.branching/merge-with-stratum-renamed.stderr b/tests.branching/merge-with-stratum-renamed.stderr
index ad144f93..ff408036 100644
--- a/tests.branching/merge-with-stratum-renamed.stderr
+++ b/tests.branching/merge-with-stratum-renamed.stderr
@@ -1 +1 @@
-ERROR: stratum goodbye-stratum was added within this branch and subsequently edited. This is not yet supported: refusing to merge.
+ERROR: goodbye-stratum.morph was not found in TMP/workspace/master/baserock:morphs at ref 804a475402fb6ded64a2749c7adf5b33c7c8ce1e