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path: root/morphlib/plugins/branch_and_merge_plugin.py
blob: d268decfaf0501720257367673d7c8d7645cdb1a (plain)
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# Copyright (C) 2012,2013,2014  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.


import cliapp
import copy
import functools
import glob
import logging
import os
import shutil
import socket
import tempfile
import time
import urlparse
import uuid

import morphlib


def warns_git_config(keys):
    def decorator(func):
        @functools.wraps(func)
        def check_config(self, *args, **kwargs):
            try:
                morphlib.git.check_config_set(self.app.runcmd, keys)
            except cliapp.AppException, e:
                self.app.status(msg="WARNING: %(message)s",
                                message=str(e), error=True)
            return func(self, *args, **kwargs)
        return check_config
        
    return decorator


warns_git_identity = warns_git_config({'user.name': 'My Name',
                                       'user.email': 'me@example.com'})


class BranchAndMergePlugin(cliapp.Plugin):

    def __init__(self):
        # Start recording changes.
        self.init_changelog()

    def enable(self):
        # User-facing commands
        self.app.add_subcommand('merge', self.merge,
                                arg_synopsis='BRANCH')
#        self.app.add_subcommand('edit', self.edit,
#                                arg_synopsis='SYSTEM STRATUM [CHUNK]')
        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('old-build', self.build,
                                arg_synopsis='SYSTEM')
        self.app.add_subcommand('old-status', self.status)
        self.app.add_subcommand('old-branch-from-image',
                                self.branch_from_image,
                                arg_synopsis='REPO BRANCH')

        # Advanced commands
        self.app.add_subcommand('old-foreach', self.foreach,
                                arg_synopsis='-- COMMAND [ARGS...]')

    def disable(self):
        pass

    def init_changelog(self):
        self.changelog = {}

    def log_change(self, repo, text):
        if not repo in self.changelog:
            self.changelog[repo] = []
        self.changelog[repo].append(text)

    def print_changelog(self, title, early_keys=[]):
        if self.changelog and self.app.settings['verbose']:
            msg = '\n%s:\n\n' % title
            keys = [x for x in early_keys if x in self.changelog]
            keys.extend([x for x in self.changelog if x not in early_keys])
            for key in keys:
                messages = self.changelog[key]
                msg += '  %s:\n' % key
                msg += '\n'.join(['    %s' % x for x in messages])
                msg += '\n\n'
            self.app.output.write(msg)

    @staticmethod
    def deduce_workspace():
        dirname = os.getcwd()
        while dirname != '/':
            dot_morph = os.path.join(dirname, '.morph')
            if os.path.isdir(dot_morph):
                return dirname
            dirname = os.path.dirname(dirname)
        raise cliapp.AppException("Can't find the workspace directory.\n"
                                  "Morph must be built and deployed within "
                                  "the system branch checkout within the "
                                  "workspace directory.")

    def deduce_system_branch(self):
        # 1. Deduce the workspace. If this fails, we're not inside a workspace.
        workspace = self.deduce_workspace()

        # 2. We're in a workspace. Check if we're inside a system branch.
        #    If we are, return its name.
        dirname = os.getcwd()
        while dirname != workspace and dirname != '/':
            if os.path.isdir(os.path.join(dirname, '.morph-system-branch')):
                branch_name = self.get_branch_config(dirname, 'branch.name')
                return branch_name, dirname
            dirname = os.path.dirname(dirname)

        # 3. We're in a workspace but not inside a branch. Try to find a
        #    branch directory in the directories below the current working
        #    directory. Avoid ambiguity by only recursing deeper if there
        #    is only one subdirectory.
        for dirname in self.walk_special_directories(
                os.getcwd(), special_subdir='.morph-system-branch',
                max_subdirs=1):
            branch_name = self.get_branch_config(dirname, 'branch.name')
            return branch_name, dirname

        raise cliapp.AppException("Can't find the system branch directory.\n"
                                  "Morph must be built and deployed within "
                                  "the system branch checkout.")

    def find_repository(self, branch_dir, repo):
        for dirname in self.walk_special_directories(branch_dir,
                                                     special_subdir='.git'):
            try:
                original_repo = self.get_repo_config(
                    dirname, 'morph.repository')
            except cliapp.AppException:
                # The user may have manually put a git repo in the branch
                continue
            if repo == original_repo:
                return dirname
        return None

    def find_system_branch(self, workspace, branch_name):
        for dirname in self.walk_special_directories(
                workspace, special_subdir='.morph-system-branch'):
            branch = self.get_branch_config(dirname, 'branch.name')
            if branch_name == branch:
                return dirname
        return None

    def set_branch_config(self, branch_dir, option, value):
        filename = os.path.join(branch_dir, '.morph-system-branch', 'config')
        self.app.runcmd(['git', 'config', '-f', filename, option, value], 
                        print_command=False)

    def get_branch_config(self, branch_dir, option):
        filename = os.path.join(branch_dir, '.morph-system-branch', 'config')
        value = self.app.runcmd(['git', 'config', '-f', filename, option], 
                                print_command=False)
        return value.strip()

    def set_repo_config(self, repo_dir, option, value):
        self.app.runcmd(['git', 'config', option, value], cwd=repo_dir, 
                        print_command=False)

    def get_repo_config(self, repo_dir, option):
        value = self.app.runcmd(['git', 'config', option], cwd=repo_dir, 
                                print_command=False)
        return value.strip()

    def get_head(self, repo_path):
        '''Return the ref that the working tree is on for a repo'''

        ref = self.app.runcmd(['git', 'rev-parse', '--abbrev-ref', 'HEAD'],
                              cwd=repo_path).strip()
        if ref == 'HEAD':
            ref = 'detached HEAD'
        return ref

    def get_uncommitted_changes(self, repo_dir, env={}):
        status = self.app.runcmd(['git', 'status', '--porcelain'],
                                 cwd=repo_dir, env=env)
        changes = []
        for change in status.strip().splitlines():
            xy, paths = change.strip().split(' ', 1)
            if xy != '??':
                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', 'rev-parse', '--verify', ref],
                                   cwd=repodir)[0:40]
        except cliapp.AppException, e:
            logging.info(
                'Ignoring error executing git rev-parse: %s' % str(e))
            return None

    def resolve_reponame(self, reponame):
        '''Return the full pull URL of a reponame.'''

        resolver = morphlib.repoaliasresolver.RepoAliasResolver(
            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.

        As a side effect, clone it into the local repo cache.

        '''

        # Setup.
        resolver = morphlib.repoaliasresolver.RepoAliasResolver(
            self.app.settings['repo-alias'])
        repo = self.get_cached_repo(reponame)

        # Make sure the parent directories needed for the repo dir exist.
        parent_dir = os.path.dirname(dirname)
        if not os.path.exists(parent_dir):
            os.makedirs(parent_dir)

        # Clone it from cache to target directory.
        target_path = os.path.abspath(dirname)
        repo.clone_checkout(ref, target_path)

        # Remember the repo name we cloned from in order to be able
        # to identify the repo again later using the same name, even
        # if the user happens to rename the directory.
        self.set_repo_config(dirname, 'morph.repository', reponame)

        # Create a UUID for the clone. We will use this for naming
        # temporary refs, e.g. for building.
        self.set_repo_config(dirname, 'morph.uuid', uuid.uuid4().hex)

        # URL configuration
        morphlib.git.set_remote(self.app.runcmd, dirname, 'origin', repo.url)
        self.set_repo_config(
            dirname, 'url.%s.pushInsteadOf' % resolver.push_url(reponame),
            resolver.pull_url(reponame))
        morphlib.git.update_submodules(self.app, target_path)

        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:
            filename = '%s.morph at ref %s in %s' % (name, ref, repo_dir)
            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)],
                                       cwd=repo_dir)
            except cliapp.AppException as e:
                msg = '%s.morph was not found in %s' % (name, repo_dir)
                if ref is not None:
                    msg += ' at ref %s' % ref
                raise cliapp.AppException(msg)

        try:
            morphology = morphlib.morph2.Morphology(text)
        except ValueError as e:
            raise morphlib.Error("Error parsing %s: %s" %
                                 (filename, str(e)))

        self._validate_morphology(morphology, '%s.morph' % name)

        return morphology

    def _validate_morphology(self, morphology, basename):
        # FIXME: This really should be in MorphologyFactory. Later.
        
        def require(field):
            if field not in morphology:
                raise morphlib.Error(
                    'Required field "%s" is missing from morphology %s' %
                        (field, basename))
        
        required = {
            'system': [
                'name',
                'arch',
                'strata',
            ],
            'stratum': [
                'name',
                'chunks',
            ],
            'chunk': [
                'name',
            ],
            'cluster': [
                'name',
                'systems',
            ],
        }
        
        also_known = {
            'system': [
                'kind',
                'description',
                'configuration-extensions',
            ],
            'stratum': [
                'kind',
                'description',
                'build-depends',
            ],
            'chunk': [
                'kind',
                'description',
                'build-system',
                'configure-commands',
                'build-commands',
                'test-commands',
                'install-commands',
                'max-jobs',
                'chunks',
                'devices',
            ],
            'cluster': [
                'kind'
            ]
        }
        
        require('kind')
        kind = morphology['kind']
        if kind not in required:
            raise morphlib.Error(
                'Unknown morphology kind "%s" in %s' % (kind, basename))
        for field in required[kind]:
            require(field)
            
        known = required[kind] + also_known[kind]
        for field in morphology.keys():
            if field not in known and not field.startswith('_orig_'):
                msg = 'Unknown field "%s" in %s' % (field, basename)
                logging.warning(msg)
                self.app.status(msg=msg)

    def reset_work_tree_safe(self, repo_dir):
        # This function avoids throwing any exceptions, so it is safe to call
        # inside an 'except' block without altering the backtrace.

        command = 'git', 'reset', '--hard'
        status, output, error = self.app.runcmd_unchecked(command,
                                                          cwd=repo_dir)
        if status != 0:
            logging.warning ("Warning: error while trying to clean up %s: %s" %
                             (repo_dir, error))

    @staticmethod
    def update_morphology(repo_dir, name, morphology, output_fd=None):
        if not name.endswith('.morph'):
            name = '%s.morph' % name
        filename = os.path.join(repo_dir, '%s' % name)
        morphology.update_file(filename, output_fd=output_fd)

        if name != morphology['name'] + '.morph':
            logging.warning('%s: morphology "name" should match filename' %
                            filename)

    @staticmethod
    def get_edit_info(morphology_name, morphology, name, collection='strata'):
        try:
            return morphology.lookup_child_by_name(name)
        except KeyError:
            if collection is 'strata':
                raise cliapp.AppException(
                        'Stratum "%s" not found in system "%s"' %
                        (name, morphology_name))
            else:
                raise cliapp.AppException(
                        'Chunk "%s" not found in stratum "%s"' %
                        (name, morphology_name))

    @staticmethod
    def convert_uri_to_path(uri):
        parts = urlparse.urlparse(uri)

        # If the URI path is relative, assume it is an aliased repo (e.g.
        # baserock:morphs). Otherwise assume it is a full URI where we need
        # to strip off the scheme and .git suffix.
        if not os.path.isabs(parts.path):
            return uri
        else:
            path = parts.netloc
            if parts.path.endswith('.git'):
                path = os.path.join(path, parts.path[1:-len('.git')])
            else:
                path = os.path.join(path, parts.path[1:])
            return path

    @staticmethod
    def remove_branch_dir_safe(workspace, branch):
        # This function avoids throwing any exceptions, so it is safe to call
        # inside an 'except' block without altering the backtrace.

        def handle_error(function, path, excinfo):
            logging.warning ("Warning: error while trying to clean up %s: %s" %
                             (path, excinfo))

        branch_dir = os.path.join(workspace, branch)
        shutil.rmtree(branch_dir, onerror=handle_error)

        # Remove parent directories that are empty too, avoiding exceptions
        parent = os.path.dirname(branch_dir)
        while parent != os.path.abspath(workspace):
            if len(os.listdir(parent)) > 0 or os.path.islink(parent):
                break
            os.rmdir(parent)
            parent = os.path.dirname(parent)

    @staticmethod
    def iterate_branch_repos(branch_path, root_repo_path):
        '''Produces a sorted list of component repos in a branch checkout'''

        dirs = [d for d in BranchAndMergePlugin.walk_special_directories(
                    branch_path, special_subdir='.git')
                if not os.path.samefile(d, root_repo_path)]
        dirs.sort()

        for d in [root_repo_path] + dirs:
            yield d

    @staticmethod
    def walk_special_directories(root_dir, special_subdir=None, max_subdirs=0):
        assert(special_subdir is not None)
        assert(max_subdirs >= 0)

        visited = set()
        for dirname, subdirs, files in os.walk(root_dir, followlinks=True):
            # Avoid infinite recursion due to symlinks.
            if dirname in visited:
                subdirs[:] = []
                continue
            visited.add(dirname)

            # Check if the current directory has the special subdirectory.
            if special_subdir in subdirs:
                yield dirname

            # Do not recurse into hidden directories.
            subdirs[:] = [x for x in subdirs if not x.startswith('.')]

            # Do not recurse if there is more than the maximum number of
            # subdirectories allowed.
            if max_subdirs > 0 and len(subdirs) > max_subdirs:
                break

    def read_metadata(self, metadata_path):
        '''Load every metadata file in `metadata_path`.
        
           Given a directory containing metadata, load them into memory
           and retain the id of the system.

           Returns the cache_key of the system and a mapping of cache_key
           to metadata.
        '''
        self.app.status(msg='Reading metadata', chatty=True)
        metadata_cache_id_lookup = {}
        system_key = None
        for path in sorted(glob.iglob(os.path.join(metadata_path, '*.meta'))):
            with open(path) as f:
                metadata = morphlib.util.json.load(f)
                cache_key = metadata['cache-key']
                metadata_cache_id_lookup[cache_key] = metadata

                if metadata['kind'] == 'system':
                    if system_key is not None:
                        raise morphlib.Error(
                            "Metadata directory contains multiple systems.")
                    system_key = cache_key

        if system_key is None:
            raise morphlib.Error(
               "Metadata directory does not contain any systems.")

        return system_key, metadata_cache_id_lookup

    def _create_branch(self, workspace, branch_name, repo, original_ref):
        '''Create a branch called branch_name based off original_ref.
           
           NOTE: self.lrc and self.rrc need to be initialized before
                 calling since clone_to_directory uses them indirectly via
                 get_cached_repo
        '''
        branch_dir = os.path.join(workspace, branch_name)
        os.makedirs(branch_dir)
        try:
            # Create a .morph-system-branch directory to clearly identify
            # this directory as a morph system branch.
            os.mkdir(os.path.join(branch_dir, '.morph-system-branch'))

            # Remember the system branch name and the repository we branched
            # off from initially.
            self.set_branch_config(branch_dir, 'branch.name', branch_name)
            self.set_branch_config(branch_dir, 'branch.root', repo)

            # Generate a UUID for the branch. We will use this for naming
            # temporary refs, e.g. building.
            self.set_branch_config(branch_dir, 'branch.uuid', uuid.uuid4().hex)

            # Clone into system branch directory.
            repo_dir = os.path.join(branch_dir, self.convert_uri_to_path(repo))
            self.clone_to_directory(repo_dir, repo, original_ref)

            # Create a new branch in the local morphs repository.
            if original_ref != branch_name:
                self.app.runcmd(['git', 'checkout', '-b', branch_name,
                                 original_ref], cwd=repo_dir)

            return branch_dir
        except BaseException, e:
            logging.error('Caught exception: %s' % str(e))
            logging.info('Removing half-finished branch %s' % branch_name)
            self.remove_branch_dir_safe(workspace, branch_name)
            raise

    def checkout_repository(self, branch_dir, repo, ref, parent_ref=None):
        '''Make a chunk or stratum repository available for a system branch

        We ensure the 'system_branch' ref within 'repo' is checked out,
        creating it from 'parent_ref' if required.

        The function aims for permissiveness, so users can try to fix any
        weirdness they have caused in the repos with another call to 'morph
        edit'.

        '''

        parent_ref = parent_ref or ref

        repo_dir = self.find_repository(branch_dir, repo)
        if repo_dir is None:
            repo_url = self.resolve_reponame(repo)
            repo_dir = os.path.join(branch_dir, self.convert_uri_to_path(repo))
            self.clone_to_directory(repo_dir, repo, parent_ref)

        if self.resolve_ref(repo_dir, ref) is None:
            self.log_change(repo, 'branch "%s" created from "%s"' %
                            (ref, parent_ref))
            command = ['git', 'checkout', '-b', ref]
        else:
            # git copes even if the system_branch ref is already checked out
            command = ['git', 'checkout', ref]

        status, output, error = self.app.runcmd_unchecked(
            command, cwd=repo_dir)
        if status != 0:
            raise cliapp.AppException('Command failed: %s in repo %s\n%s' %
                                      (' '.join(command), repo, error))
        return repo_dir

    def make_available(self, spec, branch, branch_dir, root_repo,
                       root_repo_dir):
        '''Check out the morphology that 'spec' refers to, for editing'''

        if spec.get('repo') in (None, root_repo):
            # This is only possible for stratum morphologies
            repo_dir = root_repo_dir
            if spec.get('ref') not in (None, root_repo):
                # Bring the morphology forward from its ref to the current HEAD
                repo = self.lrc.get_repo(root_repo)
                m = repo.load_morphology(spec['ref'], spec['morph'])
                self.update_morphology(root_repo_dir, spec['morph'], m)
                self.log_change(spec['repo'],
                    '"%s" copied from "%s" to "%s"' %
                    (spec['morph'], spec['ref'], branch))
        else:
            repo_dir = self.checkout_repository(
                branch_dir, spec['repo'], branch, parent_ref=spec['ref'])
        return repo_dir

    @warns_git_identity
    def edit(self, args):
        '''Edit or checkout a component in a system branch.

        Command line arguments:

        * `SYSTEM` is the name of a system morphology in the root repository
          of the current system branch.
        * `STRATUM` is the name of a stratum inside the system.
        * `CHUNK` is the name of a chunk inside the stratum.

        This marks the specified stratum or chunk (if given) as being
        changed within the system branch, by creating the git branches in
        the affected repositories, and changing the relevant morphologies
        to point at those branches. It also creates a local clone of
        the git repository of the stratum or chunk.

        For example:

            morph edit devel-system-x86-64-generic devel

        The above command will mark the `devel` stratum as being
        modified in the current system branch. In this case, the stratum's
        morphology is in the same git repository as the system morphology,
        so there is no need to create a new git branch. However, the
        system morphology is modified to point at the stratum morphology
        in the same git branch, rather than the original branch.

        In other words, where the system morphology used to say this:

            morph: devel
            repo: baserock:baserock/morphs
            ref: master

        The updated system morphology will now say this instead:

            morph: devel
            repo: baserock:baserock/morphs
            ref: jrandom/new-feature

        (Assuming the system branch is called `jrandom/new-feature`.)

        Another example:

            morph edit devel-system-x86_64-generic devel gcc

        The above command will mark the `gcc` chunk as being edited in
        the current system branch. Morph will clone the `gcc` repository
        locally, into the current workspace, and create a new (local)
        branch named after the system branch. It will also change the
        stratum morphology to refer to the new git branch, instead of
        whatever branch it was referring to originally.

        If the `gcc` repository already had a git branch named after
        the system branch, that is reused. Similarly, if the stratum
        morphology was already pointing at that branch, it doesn't
        need to be changed again. In that case, the only action Morph
        does is to clone the chunk repository locally, and if that was
        also done already, Morph does nothing.

        '''

        if len(args) not in (2, 3):
            raise cliapp.AppException(
                'morph edit must either get a system and a stratum '
                'or a system, a stratum and a chunk as arguments')

        workspace = self.deduce_workspace()
        branch, branch_dir = self.deduce_system_branch()

        # Find out which repository we branched off from.
        root_repo = self.get_branch_config(branch_dir, 'branch.root')
        root_repo_dir = self.find_repository(branch_dir, root_repo)

        system_name = args[0]
        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)

        # We need to touch every stratum in the system, not just the target
        # the user specified, because others may have build-depends that
        # point to the edited stratum.
        system_morphology = self.load_morphology(root_repo_dir, system_name)

        # Test that the specified stratum exists in the system
        self.get_edit_info(system_name, system_morphology, stratum_name)

        all_strata = system_morphology['strata']
        stratum_refs_to_correct = set()

        # Petrify the chunk
        for stratum_spec in (s for s in all_strata
                             if s['morph'] == stratum_name):
            stratum_repo_dir = self.make_available(
                stratum_spec, branch, branch_dir, root_repo, root_repo_dir)
            stratum_morphology = self.load_morphology(
                stratum_repo_dir, stratum_spec['morph'])

            if chunk_name is not None:
                # Change the stratum's ref to the chunk
                chunk_spec = self.get_edit_info(
                    stratum_name, stratum_morphology, chunk_name,
                    collection='chunks')

                if 'unpetrify-ref' in chunk_spec:
                    chunk_spec['ref'] = chunk_spec['unpetrify-ref']
                    del chunk_spec['unpetrify-ref']

                self.make_available(
                    chunk_spec, branch, branch_dir, root_repo,
                    root_repo_dir)

                if chunk_spec['ref'] != branch:
                    chunk_spec['ref'] = branch

                self.log_change(stratum_spec['repo'],
                    '"%s" now includes "%s" from "%s"' %
                    (stratum_name, chunk_name, branch))
            stratum_refs_to_correct.add((stratum_spec['repo'],
                                         stratum_spec['ref'],
                                         stratum_spec['morph']))
            # Correct the System Morphology's reference
            stratum_spec['ref'] = branch
            self.update_morphology(stratum_repo_dir, stratum_spec['morph'],
                                   stratum_morphology)
            self.log_change(root_repo,
                '"%s" now includes "%s" from "%s"' %
                (system_name, stratum_name, branch))

        # Correct all references to altered strata
        while stratum_refs_to_correct:
            repo, ref, morph = stratum_refs_to_correct.pop()
            spec = {"repo": repo, "ref": ref, "morph": morph}
            for stratum_spec in all_strata:
                changed = False
                if repo == root_repo:
                    stratum_repo_dir = root_repo_dir
                else:
                    stratum_repo_dir = self.checkout_repository(
                        branch_dir, stratum_spec['repo'],
                        branch, stratum_spec['ref'])
                stratum_morphology = self.load_morphology(
                    stratum_repo_dir, stratum_spec['morph'])
                if ('build-depends' in stratum_morphology
                    and stratum_morphology['build-depends'] is not None):
                    for bd_spec in stratum_morphology['build-depends']:
                        bd_triplet = (bd_spec['repo'],
                                      bd_spec['ref'],
                                      bd_spec['morph'])
                        if (bd_triplet == (repo, ref, morph)):
                            bd_spec['ref'] = branch
                            changed = True
                    if changed:
                        stratum_refs_to_correct.add((stratum_spec['repo'],
                                                     stratum_spec['ref'],
                                                     stratum_spec['morph']))
                        # Update the System morphology to use
                        # the modified version of the Stratum
                        stratum_spec['ref'] = branch
                        self.update_morphology(stratum_repo_dir,
                                               stratum_spec['morph'],
                                               stratum_morphology)
                        self.log_change(root_repo,
                            '"%s" now includes "%s" from "%s"' %
                            (system_name, stratum_name, branch))

        self.update_morphology(root_repo_dir, system_name, system_morphology)

        self.print_changelog('The following changes were made but have not '
                             'been committed')

    def _get_repo_name(self, alias_resolver, metadata):
        '''Attempt to find the best name for the repository.

           A defined repo-alias is preferred, but older builds may
           not have it.

           A guessed repo-alias is the next best thing, but there may
           be none or more alilases that would resolve to that URL, so
           if there are any, use the shortest as it is likely to be
           the most specific.

           If all else fails just use the URL.
        '''
        if 'repo-alias' in metadata:
            return metadata['repo-alias']

        repo_url = metadata['repo']
        aliases = alias_resolver.aliases_from_url(repo_url)

        if len(aliases) >= 1:
            # If there are multiple valid aliases, use the shortest
            return min(aliases, key=len)

        # If there are no aliases, just return the url
        return repo_url
            
    def _resolve_refs_from_metadata(self, alias_resolver,
                                    metadata_cache_id_lookup):
        '''Pre-resolve a set of refs from metadata.
        
           Resolved refs are a dict as {(repo, ref): sha1}.

           If the metadata contains the repo-alias then every
           metadata item adds the mapping of its repo-alias and ref
           to the commit it was built with.

           If the repo-alias does not exist, such as if the image was
           built before that field was added, then mappings of every
           possible repo url are added.
        '''
        resolved_refs = {}
        for md in metadata_cache_id_lookup.itervalues():
            if 'repo-alias' in md:
                repourls = [md['repo-alias']]
            else:
                repourls = [md['repo']] 
                repourls.extend(alias_resolver.aliases_from_url(md['repo']))
            for repourl in repourls:
                resolved_refs[repourl, md['original_ref']] = md['sha1']
        return resolved_refs

    def branch_from_image(self, args):
        '''Given the contents of a /baserock directory, produce a branch
           of the System, petrified to when the System was made.
        '''
        if len(args) not in (2, 3):
            raise cliapp.AppException(
                'branch-from-image needs repository, ref and path to metadata')
        root_repo = args[0]
        branch = args[1]
        metadata_path = self.app.settings['metadata-dir']
        workspace = self.deduce_workspace()
        self.lrc, self.rrc = morphlib.util.new_repo_caches(self.app)

        alias_resolver = morphlib.repoaliasresolver.RepoAliasResolver(
            self.app.settings['repo-alias'])

        system_key, metadata_cache_id_lookup = self.read_metadata(
            metadata_path)
        
        system_metadata = metadata_cache_id_lookup[system_key]
        repo = self._get_repo_name(alias_resolver, system_metadata)

        # Which repo to use? Specified or deduced?
        branch_dir = self._create_branch(workspace, branch, repo,
                                         system_metadata['sha1'])

        # Resolve refs from metadata so petrify substitutes these refs
        # into morphologies instead of the current state of the branches
        resolved_refs = self._resolve_refs_from_metadata(
            alias_resolver,
            metadata_cache_id_lookup)

        branch_root_dir = self.find_repository(branch_dir, repo)
        name = system_metadata['morphology'][:-len('.morph')]
        morphology = self.load_morphology(branch_root_dir, name)
        self.petrify_morphology(branch, branch_dir,
                                repo, branch_root_dir,
                                repo, branch_root_dir, # not a typo
                                branch, name, morphology,
                                petrified_morphologies=set(),
                                resolved_refs=resolved_refs,
                                update_working_tree=True)

    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.

        '''

        # Stratum refs are not petrified, because they must all be edited to
        # set the new chunk refs, which requires branching them all for the
        # current branch - so they will not be updated outside of the user's
        # control in any case. Chunks that have already been edited on the
        # current branch are also not petrified.

        if len(args) != 0:
            raise cliapp.AppException('morph petrify takes no arguments')

        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, os.environ, None, True)

    def unpetrify(self, args):
        '''Reverse the process of petrification.

        This undoes the changes `morph petrify` did.

        '''

        # This function makes no attempt to 'unedit' strata that were branched
        # solely so they could be petrified.

        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')
        root_repo_dir = self.find_repository(branch_path, root_repo)

        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']:
                repo_dir = self.make_available(
                    stratum_info, branch, branch_path, root_repo,
                    root_repo_dir)
                stratum_info['ref'] = branch

                stratum = self.load_morphology(repo_dir, stratum_info['morph'])

                for chunk_info in stratum['chunks']:
                    if 'unpetrify-ref' in chunk_info:
                        chunk_info['ref'] = chunk_info['unpetrify-ref']
                        del chunk_info['unpetrify-ref']
                self.update_morphology(repo_dir, stratum_info['morph'],
                                       stratum)

            self.update_morphology(root_repo_dir, name, morphology)

        self.print_changelog('The following changes were made but have not '
                             'been committed')

    @warns_git_identity
    def tag(self, args):
        '''Create an annotated Git tag of a petrified system branch.

        Command line arguments:

        * `TAG-NAME` is the name of the Git tag to be created.
        * `--` separates the Git arguments and options from the ones
          Morph parses for itself.
        * `GIT-COMMIT-ARG` is a `git commit` option or argument,
          e.g., '-m' or '-F'. These should provide the commit message.

        This command creates an annotated Git tag that points at a commit
        where all system and stratum morphologies have been petrified.
        The working tree won't be petrified, only the commit.

        Example:

            morph tag release-12.765 -- -m "Release 12.765"

        '''

        if len(args) < 1:
            raise cliapp.AppException('morph tag expects a tag name')

        tagname = args[0]

        # Deduce workspace, system branch and branch root repository.
        workspace = self.deduce_workspace()
        branch, branch_dir = self.deduce_system_branch()
        branch_root = self.get_branch_config(branch_dir, 'branch.root')
        branch_root_dir = self.find_repository(branch_dir, branch_root)

        # Prepare an environment for our internal index file.
        # This index file allows us to commit changes to a tree without
        # git noticing any change in the working tree or its own index.
        env = dict(os.environ)
        env['GIT_INDEX_FILE'] = os.path.join(
                branch_root_dir, '.git', 'morph-tag-index')

        # Extract git arguments that deal with the commit message.
        # This is so that we can use them for creating the tag commit.
        msg = None
        msg_args = []
        for i in xrange(0, len(args)):
            if args[i] == '-m' or args[i] == '-F':
                if i < len(args)-1:
                    msg_args.append(args[i])
                    msg_args.append(args[i+1])
                    if args[i] == '-m':
                        msg = args[i+1]
                    else:
                        msg = open(args[i+1]).read()
            elif args[i].startswith('--message='):
                msg_args.append(args[i])
                msg = args[i][len('--message='):]

        # Fail if no commit message was provided.
        if not msg or not msg_args:
            raise cliapp.AppException(
                    'Commit message expected. Please run one of '
                    'the following commands to provide one:\n'
                    '  morph tag NAME -- -m "Message"\n'
                    '  morph tag NAME -- --message="Message"\n'
                    '  morph tag NAME -- -F <message file>')

        # Abort if the tag already exists.
        # FIXME At the moment this only checks the local repo in the
        # workspace, not the remote repo cache or the local repo cache.
        if self.ref_exists_locally(branch_root_dir, 'refs/tags/%s' % tagname):
            raise cliapp.AppException('%s: Tag "%s" already exists' %
                                      (branch_root, tagname))

        self.app.status(msg='%(repo)s: Preparing tag commit',
                        repo=branch_root)

        # Read current tree into the internal index.
        parent_sha1 = self.resolve_ref(branch_root_dir, branch)
        self.app.runcmd(['git', 'read-tree', parent_sha1],
                        cwd=branch_root_dir, env=env)

        self.app.status(msg='%(repo)s: Petrifying everything',
                        repo=branch_root)

        # Petrify everything.
        self.lrc, self.rrc = morphlib.util.new_repo_caches(self.app)
        self.petrify_everything(branch, branch_dir,
                                branch_root, branch_root_dir,
                                tagname, env)

        self.app.status(msg='%(repo)s: Creating tag commit',
                       repo=branch_root)

        # Create a dangling commit.
        commit = self.create_tag_commit(
                branch_root_dir, tagname, msg, env)

        self.app.status(msg='%(repo)s: Creating annotated tag "%(tag)s"',
                        repo=branch_root, tag=tagname)

        # Create an annotated tag for this commit.
        self.create_annotated_tag(branch_root_dir, commit, env, args)

    def ref_exists_locally(self, repo_dir, ref):
        try:
            morphlib.git.rev_parse(self.app.runcmd, repo_dir, ref)
            return True
        except cliapp.AppException:
            return False

    def petrify_everything(self, branch, branch_dir,
            branch_root, branch_root_dir, tagref, env=os.environ,
            resolved_refs=None, update_working_tree=False):
        petrified_morphologies = set()
        resolved_refs = resolved_refs or {}
        for f in sorted(glob.iglob(os.path.join(branch_root_dir, '*.morph'))):
            name = os.path.basename(f)[:-len('.morph')]
            morphology = self.load_morphology(branch_root_dir, name)
            self.petrify_morphology(branch, branch_dir,
                                    branch_root, branch_root_dir,
                                    branch_root, branch_root_dir,
                                    tagref, name, morphology,
                                    petrified_morphologies, resolved_refs,
                                    env, update_working_tree)

    def petrify_morphology(self, branch, branch_dir,
                           branch_root, branch_root_dir, repo, repo_dir,
                           tagref, name, morphology,
                           petrified_morphologies, resolved_refs,
                           env=os.environ, update_working_tree=False):
        self.app.status(msg='%(repo)s: Petrifying morphology \"%(morph)s\"',
                        repo=repo, morph=name)

        # Mark morphology as petrified so we don't petrify it twice.
        petrified_morphologies.add(morphology)

        # Resolve the refs of all build dependencies (strata) and strata
        # in the morphology into commit SHA1s.
        strata = []
        if 'build-depends' in morphology and morphology['build-depends']:
            strata += morphology['build-depends']
        if 'strata' in morphology and morphology['strata']:
            strata += morphology['strata']
        for info in strata:
            stratum_repo_dir = self.make_available(
                    info, branch, branch_dir, repo, repo_dir)

            # Load the stratum morphology and petrify it recursively if
            # that hasn't happened yet.
            stratum = self.load_morphology(stratum_repo_dir, info['morph'])
            if not stratum in petrified_morphologies:
                self.petrify_morphology(branch, branch_dir,
                                        branch_root, branch_root_dir,
                                        info.get('repo') or branch_root,
                                        stratum_repo_dir, tagref,
                                        info['morph'], stratum,
                                        petrified_morphologies,
                                        resolved_refs, env,
                                        update_working_tree)

        # If this morphology is a stratum, resolve the refs of all its
        # chunks into SHA1s.
        if morphology['kind'] == 'stratum':
            for info in morphology['chunks']:
                commit = self.resolve_info(info, resolved_refs)
                if info['ref'] != commit:
                    info['unpetrify-ref'] = info['ref']
                    info['ref'] = commit

        # Write the petrified morphology to a temporary file in the
        # branch root repository for inclusion in the tag commit.
        with tempfile.NamedTemporaryFile(suffix='.morph') as f:
            self.update_morphology(
                    repo_dir, name, morphology, output_fd=f.file)

            # Hash the petrified morphology and add it to the index
            # for the tag commit.
            sha1 = self.app.runcmd(
                    ['git', 'hash-object', '-t', 'blob', '-w', f.name],
                    cwd=branch_root_dir, env=env)
            self.app.runcmd(
                    ['git', 'update-index', '--add', '--cacheinfo',
                     '100644', sha1, '%s.morph' % name],
                    cwd=branch_root_dir, env=env)

            # Update the working tree if requested. This can be done with
            # git-checkout-index, but we still have the file, so use that
            if update_working_tree:
                shutil.copy(f.name,
                            os.path.join(branch_root_dir, '%s.morph' % name))

    def resolve_info(self, info, resolved_refs):
        '''Takes a morphology info and resolves its ref with cache support.'''

        key = (info.get('repo'), info.get('ref'))
        if not key in resolved_refs:
            commit_sha1, tree_sha1 = self.app.resolve_ref(
                    self.lrc, self.rrc, info['repo'], info['ref'],
                    update=not self.app.settings['no-git-update'])
            resolved_refs[key] = commit_sha1
        return resolved_refs[key]

    def create_tag_commit(self, repo_dir, tagname, msg, env):
        self.app.status(msg='%(repo)s: Creating commit for the tag',
                        repo=repo_dir)

        # Write and commit the tree.
        tree = self.app.runcmd(
                ['git', 'write-tree'], cwd=repo_dir, env=env).strip()
        commit = self.app.runcmd(
                ['git', 'commit-tree', tree, '-p', 'HEAD'],
                feed_stdin=msg, cwd=repo_dir, env=env).strip()
        return commit

    def create_annotated_tag(self, repo_dir, commit, env, args=[]):
        self.app.status(msg='%(repo)s: Creating annotated tag for '
                            'commit %(commit)s',
                        repo=repo_dir, commit=commit)

        # Create an annotated tag for the commit
        self.app.runcmd(['git', 'tag', '-a'] + args + [commit],
                        cwd=repo_dir, env=env)

    # When 'merge' is unset, git doesn't try to resolve conflicts itself in
    # those files.
    MERGE_ATTRIBUTE = '*.morph\t-merge\n'

    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 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()
        if attributes == self.MERGE_ATTRIBUTE:
            os.unlink(attributes_file)
        elif attributes.endswith(self.MERGE_ATTRIBUTE):
            with morphlib.savefile.SaveFile(attributes_file, 'w') as f:
                f.write(attributes[:-len(self.MERGE_ATTRIBUTE)])

    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)
        return base_morph, from_morph, to_morph

    def check_component(self, parent_kind, parent_path, from_info, to_info):
        assert (parent_kind in ['system', 'stratum'])

        kind = 'chunk' if parent_kind == 'stratum' else 'stratum'
        name = to_info.get('alias', to_info.get('name', to_info.get('morph')))
        path = parent_path + '.' + name

        if kind == 'chunk':
            # Only chunks can be petrified
            from_unpetrify_ref = from_info.get('unpetrify-ref', None)
            to_unpetrify_ref = to_info.get('unpetrify-ref', None)
            if from_unpetrify_ref is not None and to_unpetrify_ref is None:
                self.app.output.write(
                    'WARNING: chunk "%s" is now petrified\n' % path)
            elif from_unpetrify_ref is None and to_unpetrify_ref is not None:
                self.app.output.write(
                    'WARNING: chunk "%s" is no longer petrified\n' % path)
            elif from_unpetrify_ref != to_unpetrify_ref:
                raise cliapp.AppException(
                    'merge conflict: chunk "%s" is petrified to a different '
                    'ref in each branch' % path)

    def diff_morphologies(self, path, from_morph, to_morph):
        '''Component-level diff between two versions of a morphology'''

        def component_key(info):
            # This function needs only to be stable and reproducible
            if 'name' in info:
                return (info.get('repo'), info['morph'], info['name'])
            else:
                return (info.get('repo'), info['morph'])

        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)' % path)
        if from_morph['kind'] != to_morph['kind']:
            raise cliapp.AppException(
                'merge conflict: "kind" of morphology %s changed from %s to %s'
                % (path, to_morph['kind'], from_morph['kind']))

        kind = to_morph['kind']

        # copy() makes a shallow copy, so editing the list elements will
        # change the actual morphologies.
        if kind == 'system':
            from_components = copy.copy(from_morph['strata'])
            to_components = copy.copy(to_morph['strata'])
        elif kind == 'stratum':
            from_components = copy.copy(from_morph['chunks'])
            to_components = copy.copy(to_morph['chunks'])
        from_components.sort(key=component_key)
        to_components.sort(key=component_key)

        # These are not set() purely because a set requires a hashable type
        intersection = [] # TO n FROM
        from_diff = []    # FROM \ TO
        to_diff = []      # TO \ FROM
        while len(from_components) > 0 and len(to_components) > 0:
            from_info = from_components.pop(0)
            to_info = to_components.pop(0)
            match = cmp(component_key(from_info), component_key(to_info))
            if match < 0:
                from_diff.append(from_info)
            elif match > 0:
                to_diff.append(to_info)
            elif match == 0:
                intersection.append((from_info, to_info))
        if len(from_components) != 0:
            from_diff.append(from_components.pop(0))
        if len(to_components) != 0:
            to_diff.append(to_components.pop(0))
        return intersection, from_diff, to_diff

    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

        We disable merging for morphologies and do this manually later on.

        '''

        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 self.get_uncommitted_changes(from_repo_dir) != []:
            raise cliapp.AppException('repository %s has uncommitted '
                                      'changes' % from_repo)
        if self.get_uncommitted_changes(to_repo_dir) != []:
            raise cliapp.AppException('repository %s has uncommitted '
                                      'changes' % to_repo)

        # 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', 'merge', '--no-commit', '--no-ff', from_sha1],
            cwd=to_repo_dir)
        self.enable_morph_merging(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.

        Command line arguments:

        * `BRANCH` is the name of the system branch to merge _from_.

        This merges another system branch into the current one. Morph
        will do a `git merge` for each component that has been edited,
        and undo any changes to `ref` fields in system and stratum
        morphologies that `morph edit` has made.

        You need to be in the _target_ system branch when merging. If
        you have two system branches, `TROVE_ID/release/1.2` and
        `TROVE_ID/bugfixes/12765`, and want to merge the bug fix branch
        into the release branch, you need to first checkout the release
        system branch, and then merge the bugfix branch into that.

        '''

        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)

        root_repo = self.get_branch_config(from_branch_dir, 'branch.root')
        other_root_repo = self.get_branch_config(to_branch_dir, 'branch.root')
        if root_repo != other_root_repo:
            raise cliapp.AppException('branches do not share a root '
                                      'repository : %s vs %s' %
                                      (root_repo, other_root_repo))

        def merge_chunk(parent_path, old_ci, ci):
            self.merge_repo(merged_repos,
                from_branch_dir, old_ci['repo'], from_branch,
                to_branch_dir, ci['repo'], ci['ref'])

        def merge_stratum(parent_path, old_si, si):
            path = parent_path + '.' + si['morph']

            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'])
            base_morph, from_morph, to_morph = self.get_merge_files(
                to_repo_dir, from_sha1, si['ref'], si['morph'])
            intersection, from_diff, to_diff = self.diff_morphologies(
                path, from_morph, to_morph)
            for from_ci, to_ci in intersection:
                self.check_component('stratum', path, from_ci, to_ci)

            changed = False
            edited_chunks = [ci for ci in from_morph['chunks']
                             if ci['ref'] == from_branch]
            for ci in edited_chunks:
                for old_ci in to_morph['chunks']:
                    if old_ci['repo'] == ci['repo']:
                        break
                else:
                    raise cliapp.AppException(
                        'chunk %s was added within this branch and '
                        'subsequently edited. This is not yet supported: '
                        'refusing to merge.' % ci['name'])
                changed = True
                ci['ref'] = old_ci['ref']
                merge_chunk(path, old_ci, ci)
            if changed:
                self.update_morphology(to_repo_dir, si['morph'], to_morph)
                self.app.runcmd(['git', 'add', si['morph'] + '.morph'],
                                cwd=to_repo_dir)

        def merge_system(name):
            base_morph, from_morph, to_morph = self.get_merge_files(
                to_root_dir, from_sha1, to_branch, name)
            if to_morph['kind'] != 'system':
                return

            intersection, from_diff, to_diff = self.diff_morphologies(
                name, from_morph, to_morph)
            for from_si, to_si in intersection:
                self.check_component('system', name, from_si, to_si)

            changed = False
            edited_strata = [si for si in from_morph['strata']
                             if si.get('ref') == from_branch]
            for si in edited_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.get('repo') == si.get('repo')):
                        break
                else:
                    raise cliapp.AppException(
                        'stratum %s was added within this branch and '
                        'subsequently edited. This is not yet supported: '
                        'refusing to merge.' % si['morph'])
                changed = True
                si['ref'] = old_si.get('ref')
                merge_stratum(name, old_si, si)
            if changed:
                self.update_morphology(to_root_dir, name, to_morph)
                self.app.runcmd(['git', 'add', f], cwd=to_root_dir)

        merged_repos = {}
        try:
            to_root_dir, from_sha1 = self.merge_repo(merged_repos,
                from_branch_dir, root_repo, from_branch,
                to_branch_dir, root_repo, to_branch)

            for f in sorted(glob.iglob(os.path.join(to_root_dir, '*.morph'))):
                name = os.path.basename(f)[:-len('.morph')]
                merge_system(name)

            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 BaseException, e:
            logging.error('Caught exception: %s' % str(e))
            logging.info('Resetting half-finished merge')
            for repo_dir, sha1 in merged_repos.itervalues():
                self.reset_work_tree_safe(repo_dir)
            raise

    def build(self, args):
        '''Build a system image in the current system branch

        Command line arguments:

        * `SYSTEM` is the name of the system to build.

        This builds a system image, and any of its components that
        need building.  The system name is the basename of the system
        morphology, in the root repository of the current system branch,
        without the `.morph` suffix in the filename.

        The location of the resulting system image artifact is printed
        at the end of the build output.

        You do not need to commit your changes before building, Morph
        does that for you, in a temporary branch for each build. However,
        note that Morph does not untracked files to the temporary branch,
        only uncommitted changes to files git already knows about. You
        need to `git add` and commit each new file yourself.

        Example:

            morph build devel-system-x86_64-generic

        '''

        if len(args) != 1:
            raise cliapp.AppException('morph build expects exactly one '
                                      'parameter: the system to build')

        # Raise an exception if there is not enough space
        morphlib.util.check_disk_available(
            self.app.settings['tempdir'],
            self.app.settings['tempdir-min-space'],
            self.app.settings['cachedir'],
            self.app.settings['cachedir-min-space'])

        system_name = args[0]

        # Deduce workspace and system branch and branch root repository.
        workspace = self.deduce_workspace()
        branch, branch_dir = self.deduce_system_branch()
        branch_root = self.get_branch_config(branch_dir, 'branch.root')
        branch_uuid = self.get_branch_config(branch_dir, 'branch.uuid')

        # Generate a UUID for the build.
        build_uuid = uuid.uuid4().hex

        build_command = morphlib.buildcommand.BuildCommand(self.app)
        build_command = self.app.hookmgr.call('new-build-command',
                                              build_command)
        push = self.app.settings['push-build-branches']

        self.app.status(msg='Starting build %(uuid)s', uuid=build_uuid)

        self.app.status(msg='Collecting morphologies involved in '
                            'building %(system)s from %(branch)s',
                            system=system_name, branch=branch)

        # Get repositories of morphologies involved in building this system
        # from the current system branch.
        build_repos = self.get_system_build_repos(
                branch, branch_dir, branch_root, system_name)

        # Generate temporary build ref names for all these repositories.
        self.generate_build_ref_names(build_repos, branch_uuid)

        # Create the build refs for all these repositories and commit
        # all uncommitted changes to them, updating all references
        # to system branch refs to point to the build refs instead.
        self.update_build_refs(build_repos, branch, build_uuid, push)

        if push:
            self.push_build_refs(build_repos)
            build_branch_root = branch_root
        else:
            dirname = build_repos[branch_root]['dirname']
            build_branch_root = urlparse.urljoin('file://', dirname)

        # Run the build.
        build_command.build([build_branch_root,
                             build_repos[branch_root]['build-ref'],
                             system_name])

        if push:
            self.delete_remote_build_refs(build_repos)

        self.app.status(msg='Finished build %(uuid)s', uuid=build_uuid)

    def get_system_build_repos(self, system_branch, branch_dir,
                               branch_root, system_name):
        '''Map upstream repository URLs to their checkouts in the system branch

        Also provides the list of morphologies stored in each repository,
        grouped by kind.

        '''

        build_repos = {}

        def prepare_repo_info(repo, dirname):
            build_repos[repo] = {
                'dirname': dirname,
                'systems': [],
                'strata': [],
                'chunks': []
            }

        def add_morphology_info(info, category):
            repo = info['repo'] or branch_root
            if repo in build_repos:
                repo_dir = build_repos[repo]['dirname']
            else:
                repo_dir = self.find_repository(branch_dir, repo)
            if repo_dir:
                if not repo in build_repos:
                    prepare_repo_info(repo, repo_dir)
                build_repos[repo][category].append(info['morph'])
            return repo_dir

        # Add repository and morphology of the system.
        branch_root_dir = self.find_repository(branch_dir, branch_root)
        prepare_repo_info(branch_root, branch_root_dir)
        build_repos[branch_root]['systems'].append(system_name)

        # Traverse and add repositories and morphologies involved in
        # building this system from the system branch.
        system_morphology = self.load_morphology(branch_root_dir, system_name)
        for info in system_morphology['strata']:
            if info['ref'] == system_branch or info['ref'] is None:
                repo_dir = add_morphology_info(info, 'strata')
                if repo_dir:
                    stratum_morphology = self.load_morphology(
                            repo_dir, info['morph'])
                    for info in stratum_morphology['chunks']:
                        if info['ref'] == system_branch:
                            add_morphology_info(info, 'chunks')

        return build_repos

    def inject_build_refs(self, morphology, build_repos, will_push):
        # Starting from a system or stratum morphology, update all ref
        # pointers of strata or chunks involved in a system build (represented
        # by build_repos) to point to temporary build refs of the repos
        # involved in the system build.
        def inject_build_ref(info):
            if info['repo'] in build_repos and (
                    info['morph'] in build_repos[info['repo']]['strata'] or
                    info['morph'] in build_repos[info['repo']]['chunks']):
                info['ref'] = build_repos[info['repo']]['build-ref']
                if not will_push:
                    dirname = build_repos[info['repo']]['dirname']
                    info['repo'] = urlparse.urljoin('file://', dirname)
        if morphology['kind'] == 'system':
            for info in morphology['strata']:
                inject_build_ref(info)
        elif morphology['kind'] == 'stratum':
            if morphology['build-depends'] is not None:
                for info in morphology['build-depends']:
                    inject_build_ref(info)
            for info in morphology['chunks']:
                inject_build_ref(info)

    def generate_build_ref_names(self, build_repos, branch_uuid):
        for repo, info in build_repos.iteritems():
            repo_dir = info['dirname']
            repo_uuid = self.get_repo_config(repo_dir, 'morph.uuid')
            build_ref = os.path.join(self.app.settings['build-ref-prefix'],
                                     branch_uuid, repo_uuid)
            info['build-ref'] = build_ref

    def update_build_refs(self, build_repos, system_branch, build_uuid,
                          will_push):
        '''Update build branches for each repository with any local changes '''

        # Define the committer.
        committer_name = 'Morph (on behalf of %s)' % \
            (morphlib.git.get_user_name(self.app.runcmd))
        committer_email = morphlib.git.get_user_email(self.app.runcmd)

        for repo, info in build_repos.iteritems():
            repo_dir = info['dirname']
            build_ref = info['build-ref']

            self.app.status(msg='%(repo)s: Creating build branch', repo=repo)

            # Obtain parent SHA1 for the temporary ref tree to be committed.
            # This will either be the current commit of the temporary ref or
            # HEAD in case the temporary ref does not exist yet.
            system_branch_sha1 = self.resolve_ref(
                repo_dir, '%s^{commit}' % system_branch)
            parent_sha1 = self.resolve_ref(repo_dir, '%s^{commit}' % build_ref)
            if not parent_sha1:
                parent_sha1 = system_branch_sha1

            # Prepare an environment with our internal index file.
            # This index file allows us to commit changes to a tree without
            # git noticing any change in working tree or its own index.
            env = dict(os.environ)
            env['GIT_INDEX_FILE'] = os.path.join(
                    repo_dir, '.git', 'morph-index')
            env['GIT_COMMITTER_NAME'] = committer_name
            env['GIT_COMMITTER_EMAIL'] = committer_email

            # Read tree from current HEAD into the morph index.
            self.app.runcmd(['git', 'read-tree', system_branch_sha1],
                            cwd=repo_dir, env=env)

            self.app.status(msg='%(repo)s: Adding uncommitted changes to '
                                'build branch', repo=repo)

            # Add all local, uncommitted changes to our internal index.
            changed_files = self.get_uncommitted_changes(repo_dir, env)
            self.app.runcmd(['git', 'add'] + changed_files,
                            cwd=repo_dir, env=env)

            self.app.status(msg='%(repo)s: Updating morphologies to use '
                                'build branch instead of "%(branch)s"',
                            repo=repo, branch=system_branch)

            # Update all references to the system branches of strata
            # and chunks to point to the temporary refs, which is needed
            # for building.
            filenames = info['systems'] + info['strata']
            for filename in filenames:
                # Inject temporary refs in the right places in each morphology.
                morphology = self.load_morphology(repo_dir, filename)
                self.inject_build_refs(morphology, build_repos, will_push)
                with tempfile.NamedTemporaryFile(suffix='.morph') as f:
                    self.update_morphology(
                            repo_dir, filename, morphology, output_fd=f.file)

                    morphology_sha1 = self.app.runcmd(
                            ['git', 'hash-object', '-t', 'blob', '-w', f.name],
                            cwd=repo_dir, env=env)

                    try:
                        self.app.runcmd(
                            ['git', 'update-index', '--cacheinfo',
                             '100644', morphology_sha1, '%s.morph' % filename],
                            cwd=repo_dir, env=env)
                    except cliapp.AppException, e:
                        raise cliapp.AppException(
                            "You seem to want to build %s, but '%s.morph' "
                            "doesn't exist in the morphologies repository. "
                            "Did you forget to commit it?" %
                            (filename, filename))

            # Create a commit message including the build UUID. This allows us
            # to collect all commits of a build across repositories and thereby
            # see the changes made to the entire system between any two builds.
            message = 'Morph build %s\n\nSystem branch: %s\n' % \
                      (build_uuid, system_branch)

            # Write and commit the tree and update the temporary build ref.
            tree = self.app.runcmd(
                    ['git', 'write-tree'], cwd=repo_dir, env=env).strip()
            commit = self.app.runcmd(
                    ['git', 'commit-tree', tree, '-p', parent_sha1],
                     feed_stdin=message, cwd=repo_dir, env=env).strip()
            self.app.runcmd(
                    ['git', 'update-ref', '-m', message,
                     'refs/heads/%s' % build_ref, commit],
                    cwd=repo_dir, env=env)

    def push_build_refs(self, build_repos):
        for repo, info in build_repos.iteritems():
            self.app.status(msg='%(repo)s: Pushing build branch', repo=repo)
            self.app.runcmd(['git', 'push', 'origin', '%s:%s' %
                             (info['build-ref'], info['build-ref'])],
                            cwd=info['dirname'])

    def delete_remote_build_refs(self, build_repos):
        for repo, info in build_repos.iteritems():
            self.app.status(msg='%(repo)s: Deleting remote build branch',
                            repo=repo)
            self.app.runcmd(['git', 'push', 'origin',
                             ':%s' % info['build-ref']], cwd=info['dirname'])

    def status(self, args):
        '''Show information about the current system branch or workspace

        This shows the status of every local git repository of the
        current system branch. This is similar to running `git status`
        in each repository separately, but the output is nicer.

        If run in a Morph workspace, but not in a system branch checkout,
        it lists all checked out system branches in the workspace.

        '''

        if len(args) != 0:
            raise cliapp.AppException('morph status takes no arguments')

        workspace = self.deduce_workspace()
        try:
            branch, branch_path = self.deduce_system_branch()
        except cliapp.AppException:
            branch = None

        if branch is None:
            self.app.output.write("System branches in current workspace:\n")
            branch_dirs = sorted(self.walk_special_directories(
                workspace, special_subdir='.morph-system-branch'))
            for dirname in branch_dirs:
                branch = self.get_branch_config(dirname, 'branch.name')
                self.app.output.write("    %s\n" % branch)
            return

        root_repo = self.get_branch_config(branch_path, 'branch.root')
        root_repo_path = self.find_repository(branch_path, root_repo)

        self.app.output.write("On branch %s, root %s\n" % (branch, root_repo))

        has_uncommitted_changes = False
        for d in self.iterate_branch_repos(branch_path, root_repo_path):
            try:
                repo = self.get_repo_config(d, 'morph.repository')
            except cliapp.AppException:
                self.app.output.write(
                    '    %s: not part of system branch\n' % d)
                continue
            head = self.get_head(d)
            if head != branch:
                self.app.output.write(
                    '    %s: unexpected ref checked out "%s"\n' % (repo, head))
            if len(self.get_uncommitted_changes(d)) > 0:
                has_uncommitted_changes = True
                self.app.output.write('    %s: uncommitted changes\n' % repo)

        if not has_uncommitted_changes:
            self.app.output.write("\nNo repos have outstanding changes.\n")

    def foreach(self, args):
        '''Run a command in each repository checked out in a system branch.

        Use -- before specifying the command to separate its arguments from
        Morph's own arguments.

        Command line arguments:

        * `--` indicates the end of option processing for Morph.
        * `COMMAND` is a command to run.
        * `ARGS` is a list of arguments or options to be passed onto
          `COMMAND`.

        This runs the given `COMMAND` in each git repository belonging
        to the current system branch that exists locally in the current
        workspace.  This can be a handy way to do the same thing in all
        the local git repositories.

        For example:

            morph foreach -- git push

        The above command would push any committed changes in each
        repository to the git server.

        '''

        # For simplicity, this simply iterates repositories in the directory
        # rather than walking through the morphologies as 'morph merge' does.

        if len(args) == 0:
            raise cliapp.AppException('morph foreach expects a command to run')

        workspace = self.deduce_workspace()
        branch, branch_path = self.deduce_system_branch()

        root_repo = self.get_branch_config(branch_path, 'branch.root')
        root_repo_path = self.find_repository(branch_path, root_repo)

        for d in self.iterate_branch_repos(branch_path, root_repo_path):
            try:
                repo = self.get_repo_config(d, 'morph.repository')
            except cliapp.AppException:
                continue

            if d != root_repo_path:
                self.app.output.write('\n')
            self.app.output.write('%s\n' % repo)

            status, output, error = self.app.runcmd_unchecked(args, cwd=d)
            self.app.output.write(output)
            if status != 0:
                self.app.output.write(error)
                raise cliapp.AppException(
                    'Command failed at repo %s: %s' % (repo, ' '.join(args)))