diff --git a/command.py b/command.py
index 287f4d3..207ef46 100644
--- a/command.py
+++ b/command.py
@@ -129,7 +129,7 @@
   def GetProjects(self, args, missing_ok=False, submodules_ok=False):
     """A list of projects that match the arguments.
     """
-    all_projects = self.manifest.projects
+    all_projects_list = self.manifest.projects
     result = []
 
     mp = self.manifest.manifestProject
@@ -140,7 +140,6 @@
     groups = [x for x in re.split(r'[,\s]+', groups) if x]
 
     if not args:
-      all_projects_list = list(all_projects.values())
       derived_projects = {}
       for project in all_projects_list:
         if submodules_ok or project.sync_s:
@@ -152,12 +151,12 @@
             project.MatchesGroups(groups)):
           result.append(project)
     else:
-      self._ResetPathToProjectMap(all_projects.values())
+      self._ResetPathToProjectMap(all_projects_list)
 
       for arg in args:
-        project = all_projects.get(arg)
+        projects = self.manifest.GetProjectsWithName(arg)
 
-        if not project:
+        if not projects:
           path = os.path.abspath(arg).replace('\\', '/')
           project = self._GetProjectByPath(path)
 
@@ -172,14 +171,19 @@
             if search_again:
               project = self._GetProjectByPath(path) or project
 
-        if not project:
-          raise NoSuchProjectError(arg)
-        if not missing_ok and not project.Exists:
-          raise NoSuchProjectError(arg)
-        if not project.MatchesGroups(groups):
-          raise InvalidProjectGroupsError(arg)
+          if project:
+            projects = [project]
 
-        result.append(project)
+        if not projects:
+          raise NoSuchProjectError(arg)
+
+        for project in projects:
+          if not missing_ok and not project.Exists:
+            raise NoSuchProjectError(arg)
+          if not project.MatchesGroups(groups):
+            raise InvalidProjectGroupsError(arg)
+
+        result.extend(projects)
 
     def _getpath(x):
       return x.relpath
diff --git a/manifest_xml.py b/manifest_xml.py
index bdbb1d4..647e89f 100644
--- a/manifest_xml.py
+++ b/manifest_xml.py
@@ -209,8 +209,9 @@
       root.appendChild(doc.createTextNode(''))
 
     def output_projects(parent, parent_node, projects):
-      for p in projects:
-        output_project(parent, parent_node, self.projects[p])
+      for project_name in projects:
+        for project in self._projects[project_name]:
+          output_project(parent, parent_node, project)
 
     def output_project(parent, parent_node, p):
       if not p.MatchesGroups(groups):
@@ -269,13 +270,11 @@
         e.setAttribute('sync-s', 'true')
 
       if p.subprojects:
-        sort_projects = list(sorted([subp.name for subp in p.subprojects]))
-        output_projects(p, e, sort_projects)
+        subprojects = set(subp.name for subp in p.subprojects)
+        output_projects(p, e, list(sorted(subprojects)))
 
-    sort_projects = list(sorted([key for key, value in self.projects.items()
-                     if not value.parent]))
-    sort_projects.sort()
-    output_projects(None, root, sort_projects)
+    projects = set(p.name for p in self._paths.values() if not p.parent)
+    output_projects(None, root, list(sorted(projects)))
 
     if self._repo_hooks_project:
       root.appendChild(doc.createTextNode(''))
@@ -288,9 +287,14 @@
     doc.writexml(fd, '', '  ', '\n', 'UTF-8')
 
   @property
+  def paths(self):
+    self._Load()
+    return self._paths
+
+  @property
   def projects(self):
     self._Load()
-    return self._projects
+    return self._paths.values()
 
   @property
   def remotes(self):
@@ -324,6 +328,7 @@
   def _Unload(self):
     self._loaded = False
     self._projects = {}
+    self._paths = {}
     self._remotes = {}
     self._default = None
     self._repo_hooks_project = None
@@ -453,11 +458,17 @@
         self._manifest_server = url
 
     def recursively_add_projects(project):
-      if self._projects.get(project.name):
+      projects = self._projects.setdefault(project.name, [])
+      if project.relpath is None:
         raise ManifestParseError(
-            'duplicate project %s in %s' %
+            'missing path for %s in %s' %
             (project.name, self.manifestFile))
-      self._projects[project.name] = project
+      if project.relpath in self._paths:
+        raise ManifestParseError(
+            'duplicate path %s in %s' %
+            (project.relpath, self.manifestFile))
+      self._paths[project.relpath] = project
+      projects.append(project)
       for subproject in project.subprojects:
         recursively_add_projects(subproject)
 
@@ -478,12 +489,18 @@
 
         # Store a reference to the Project.
         try:
-          self._repo_hooks_project = self._projects[repo_hooks_project]
+          repo_hooks_projects = self._projects[repo_hooks_project]
         except KeyError:
           raise ManifestParseError(
               'project %s not found for repo-hooks' %
               (repo_hooks_project))
 
+        if len(repo_hooks_projects) != 1:
+          raise ManifestParseError(
+              'internal error parsing repo-hooks in %s' %
+              (self.manifestFile))
+        self._repo_hooks_project = repo_hooks_projects[0]
+
         # Store the enabled hooks in the Project object.
         self._repo_hooks_project.enabled_repo_hooks = enabled_repo_hooks
       if node.nodeName == 'remove-project':
@@ -530,11 +547,12 @@
                         name = name,
                         remote = remote.ToRemoteSpec(name),
                         gitdir = gitdir,
+                        objdir = gitdir,
                         worktree = None,
                         relpath = None,
                         revisionExpr = m.revisionExpr,
                         revisionId = None)
-      self._projects[project.name] = project
+      self._projects[project.name] = [project]
 
   def _ParseRemote(self, node):
     """
@@ -694,9 +712,10 @@
     groups = [x for x in re.split(r'[,\s]+', groups) if x]
 
     if parent is None:
-      relpath, worktree, gitdir = self.GetProjectPaths(name, path)
+      relpath, worktree, gitdir, objdir = self.GetProjectPaths(name, path)
     else:
-      relpath, worktree, gitdir = self.GetSubprojectPaths(parent, path)
+      relpath, worktree, gitdir, objdir = \
+          self.GetSubprojectPaths(parent, name, path)
 
     default_groups = ['all', 'name:%s' % name, 'path:%s' % relpath]
     groups.extend(set(default_groups).difference(groups))
@@ -709,6 +728,7 @@
                       name = name,
                       remote = remote.ToRemoteSpec(name),
                       gitdir = gitdir,
+                      objdir = objdir,
                       worktree = worktree,
                       relpath = relpath,
                       revisionExpr = revisionExpr,
@@ -737,10 +757,15 @@
     if self.IsMirror:
       worktree = None
       gitdir = os.path.join(self.topdir, '%s.git' % name)
+      objdir = gitdir
     else:
       worktree = os.path.join(self.topdir, path).replace('\\', '/')
       gitdir = os.path.join(self.repodir, 'projects', '%s.git' % path)
-    return relpath, worktree, gitdir
+      objdir = os.path.join(self.repodir, 'project-objects', '%s.git' % name)
+    return relpath, worktree, gitdir, objdir
+
+  def GetProjectsWithName(self, name):
+    return self._projects.get(name, [])
 
   def GetSubprojectName(self, parent, submodule_path):
     return os.path.join(parent.name, submodule_path)
@@ -751,14 +776,15 @@
   def _UnjoinRelpath(self, parent_relpath, relpath):
     return os.path.relpath(relpath, parent_relpath)
 
-  def GetSubprojectPaths(self, parent, path):
+  def GetSubprojectPaths(self, parent, name, path):
     relpath = self._JoinRelpath(parent.relpath, path)
     gitdir = os.path.join(parent.gitdir, 'subprojects', '%s.git' % path)
+    objdir = os.path.join(parent.gitdir, 'subproject-objects', '%s.git' % name)
     if self.IsMirror:
       worktree = None
     else:
       worktree = os.path.join(parent.worktree, path).replace('\\', '/')
-    return relpath, worktree, gitdir
+    return relpath, worktree, gitdir, objdir
 
   def _ParseCopyFile(self, project, node):
     src = self._reqatt(node, 'src')
diff --git a/project.py b/project.py
index dec21ab..f9f1f75 100644
--- a/project.py
+++ b/project.py
@@ -487,6 +487,7 @@
                name,
                remote,
                gitdir,
+               objdir,
                worktree,
                relpath,
                revisionExpr,
@@ -507,6 +508,7 @@
       name: The `name` attribute of manifest.xml's project element.
       remote: RemoteSpec object specifying its remote's properties.
       gitdir: Absolute path of git directory.
+      objdir: Absolute path of directory to store git objects.
       worktree: Absolute path of git working tree.
       relpath: Relative path of git working tree to repo's top directory.
       revisionExpr: The `revision` attribute of manifest.xml's project element.
@@ -525,6 +527,7 @@
     self.name = name
     self.remote = remote
     self.gitdir = gitdir.replace('\\', '/')
+    self.objdir = objdir.replace('\\', '/')
     if worktree:
       self.worktree = worktree.replace('\\', '/')
     else:
@@ -557,11 +560,12 @@
                     defaults =  self.manifest.globalConfig)
 
     if self.worktree:
-      self.work_git = self._GitGetByExec(self, bare=False)
+      self.work_git = self._GitGetByExec(self, bare=False, gitdir=gitdir)
     else:
       self.work_git = None
-    self.bare_git = self._GitGetByExec(self, bare=True)
+    self.bare_git = self._GitGetByExec(self, bare=True, gitdir=gitdir)
     self.bare_ref = GitRefs(gitdir)
+    self.bare_objdir = self._GitGetByExec(self, bare=True, gitdir=objdir)
     self.dest_branch = dest_branch
 
     # This will be filled in if a project is later identified to be the
@@ -1069,6 +1073,7 @@
     """Perform only the local IO portion of the sync process.
        Network access is not required.
     """
+    self._InitWorkTree()
     all_refs = self.bare_ref.all
     self.CleanPublishedCache(all_refs)
     revid = self.GetRevisionId(all_refs)
@@ -1077,7 +1082,6 @@
       self._FastForward(revid)
       self._CopyFiles()
 
-    self._InitWorkTree()
     head = self.work_git.GetHead()
     if head.startswith(R_HEADS):
       branch = head[len(R_HEADS):]
@@ -1544,11 +1548,13 @@
       return result
     for rev, path, url in self._GetSubmodules():
       name = self.manifest.GetSubprojectName(self, path)
-      project = self.manifest.projects.get(name)
+      relpath, worktree, gitdir, objdir = \
+          self.manifest.GetSubprojectPaths(self, name, path)
+      project = self.manifest.paths.get(relpath)
       if project:
         result.extend(project.GetDerivedSubprojects())
         continue
-      relpath, worktree, gitdir = self.manifest.GetSubprojectPaths(self, path)
+
       remote = RemoteSpec(self.remote.name,
                           url = url,
                           review = self.remote.review)
@@ -1556,6 +1562,7 @@
                            name = name,
                            remote = remote,
                            gitdir = gitdir,
+                           objdir = objdir,
                            worktree = worktree,
                            relpath = relpath,
                            revisionExpr = self.revisionExpr,
@@ -1905,8 +1912,17 @@
 
   def _InitGitDir(self, mirror_git=None):
     if not os.path.exists(self.gitdir):
-      os.makedirs(self.gitdir)
-      self.bare_git.init()
+
+      # Initialize the bare repository, which contains all of the objects.
+      if not os.path.exists(self.objdir):
+        os.makedirs(self.objdir)
+        self.bare_objdir.init()
+
+      # If we have a separate directory to hold refs, initialize it as well.
+      if self.objdir != self.gitdir:
+        os.makedirs(self.gitdir)
+        self._ReferenceGitDir(self.objdir, self.gitdir, share_refs=False,
+                              copy_all=True)
 
       mp = self.manifest.manifestProject
       ref_dir = mp.config.GetString('repo.reference') or ''
@@ -2022,33 +2038,61 @@
         msg = 'manifest set to %s' % self.revisionExpr
         self.bare_git.symbolic_ref('-m', msg, ref, dst)
 
+  def _ReferenceGitDir(self, gitdir, dotgit, share_refs, copy_all):
+    """Update |dotgit| to reference |gitdir|, using symlinks where possible.
+
+    Args:
+      gitdir: The bare git repository. Must already be initialized.
+      dotgit: The repository you would like to initialize.
+      share_refs: If true, |dotgit| will store its refs under |gitdir|.
+          Only one work tree can store refs under a given |gitdir|.
+      copy_all: If true, copy all remaining files from |gitdir| -> |dotgit|.
+          This saves you the effort of initializing |dotgit| yourself.
+    """
+    # These objects can be shared between several working trees.
+    symlink_files = ['description', 'info']
+    symlink_dirs = ['hooks', 'objects', 'rr-cache', 'svn']
+    if share_refs:
+      # These objects can only be used by a single working tree.
+      symlink_files += ['config', 'packed-refs']
+      symlink_dirs += ['logs', 'refs']
+    to_symlink = symlink_files + symlink_dirs
+
+    to_copy = []
+    if copy_all:
+      to_copy = os.listdir(gitdir)
+
+    for name in set(to_copy).union(to_symlink):
+      try:
+        src = os.path.realpath(os.path.join(gitdir, name))
+        dst = os.path.realpath(os.path.join(dotgit, name))
+
+        if os.path.lexists(dst) and not os.path.islink(dst):
+          raise GitError('cannot overwrite a local work tree')
+
+        # If the source dir doesn't exist, create an empty dir.
+        if name in symlink_dirs and not os.path.lexists(src):
+          os.makedirs(src)
+
+        if name in to_symlink:
+          os.symlink(os.path.relpath(src, os.path.dirname(dst)), dst)
+        elif copy_all and not os.path.islink(dst):
+          if os.path.isdir(src):
+            shutil.copytree(src, dst)
+          elif os.path.isfile(src):
+            shutil.copy(src, dst)
+      except OSError as e:
+        if e.errno == errno.EPERM:
+          raise GitError('filesystem must support symlinks')
+        else:
+          raise
+
   def _InitWorkTree(self):
     dotgit = os.path.join(self.worktree, '.git')
     if not os.path.exists(dotgit):
       os.makedirs(dotgit)
-
-      for name in ['config',
-                   'description',
-                   'hooks',
-                   'info',
-                   'logs',
-                   'objects',
-                   'packed-refs',
-                   'refs',
-                   'rr-cache',
-                   'svn']:
-        try:
-          src = os.path.join(self.gitdir, name)
-          dst = os.path.join(dotgit, name)
-          if os.path.islink(dst) or not os.path.exists(dst):
-            os.symlink(os.path.relpath(src, os.path.dirname(dst)), dst)
-          else:
-            raise GitError('cannot overwrite a local work tree')
-        except OSError as e:
-          if e.errno == errno.EPERM:
-            raise GitError('filesystem must support symlinks')
-          else:
-            raise
+      self._ReferenceGitDir(self.gitdir, dotgit, share_refs=True,
+                            copy_all=False)
 
       _lwrite(os.path.join(dotgit, HEAD), '%s\n' % self.GetRevisionId())
 
@@ -2058,14 +2102,10 @@
       if GitCommand(self, cmd).Wait() != 0:
         raise GitError("cannot initialize work tree")
 
-      rr_cache = os.path.join(self.gitdir, 'rr-cache')
-      if not os.path.exists(rr_cache):
-        os.makedirs(rr_cache)
-
       self._CopyFiles()
 
   def _gitdir_path(self, path):
-    return os.path.join(self.gitdir, path)
+    return os.path.realpath(os.path.join(self.gitdir, path))
 
   def _revlist(self, *args, **kw):
     a = []
@@ -2078,9 +2118,10 @@
     return self.bare_ref.all
 
   class _GitGetByExec(object):
-    def __init__(self, project, bare):
+    def __init__(self, project, bare, gitdir):
       self._project = project
       self._bare = bare
+      self._gitdir = gitdir
 
     def LsOthers(self):
       p = GitCommand(self._project,
@@ -2089,6 +2130,7 @@
                       '--others',
                       '--exclude-standard'],
                      bare = False,
+                     gitdir=self._gitdir,
                      capture_stdout = True,
                      capture_stderr = True)
       if p.Wait() == 0:
@@ -2104,6 +2146,7 @@
       cmd.extend(args)
       p = GitCommand(self._project,
                      cmd,
+                     gitdir=self._gitdir,
                      bare = False,
                      capture_stdout = True,
                      capture_stderr = True)
@@ -2213,6 +2256,7 @@
       p = GitCommand(self._project,
                      cmdv,
                      bare = self._bare,
+                     gitdir=self._gitdir,
                      capture_stdout = True,
                      capture_stderr = True)
       r = []
@@ -2265,6 +2309,7 @@
         p = GitCommand(self._project,
                        cmdv,
                        bare = self._bare,
+                       gitdir=self._gitdir,
                        capture_stdout = True,
                        capture_stderr = True)
         if p.Wait() != 0:
@@ -2398,6 +2443,7 @@
                      manifest = manifest,
                      name = name,
                      gitdir = gitdir,
+                     objdir = gitdir,
                      worktree = worktree,
                      remote = RemoteSpec('origin'),
                      relpath = '.repo/%s' % name,
diff --git a/subcmds/rebase.py b/subcmds/rebase.py
index b9a7774..1bdc1f0 100644
--- a/subcmds/rebase.py
+++ b/subcmds/rebase.py
@@ -62,6 +62,9 @@
     if opt.interactive and not one_project:
       print('error: interactive rebase not supported with multiple projects',
             file=sys.stderr)
+      if len(args) == 1:
+        print('note: project %s is mapped to more than one path' % (args[0],),
+            file=sys.stderr)
       return -1
 
     for project in all_projects:
diff --git a/subcmds/sync.py b/subcmds/sync.py
index e9d52b7..d1a0641 100644
--- a/subcmds/sync.py
+++ b/subcmds/sync.py
@@ -219,9 +219,25 @@
                  dest='repo_upgraded', action='store_true',
                  help=SUPPRESS_HELP)
 
-  def _FetchHelper(self, opt, project, lock, fetched, pm, sem, err_event):
+  def _FetchProjectList(self, opt, projects, *args):
     """Main function of the fetch threads when jobs are > 1.
 
+    Delegates most of the work to _FetchHelper.
+
+    Args:
+      opt: Program options returned from optparse.  See _Options().
+      projects: Projects to fetch.
+      *args: Remaining arguments to pass to _FetchHelper. See the
+          _FetchHelper docstring for details.
+    """
+    for project in projects:
+      success = self._FetchHelper(opt, project, *args)
+      if not success and not opt.force_broken:
+        break
+
+  def _FetchHelper(self, opt, project, lock, fetched, pm, sem, err_event):
+    """Fetch git objects for a single project.
+
     Args:
       opt: Program options returned from optparse.  See _Options().
       project: Project object for the project to fetch.
@@ -235,6 +251,9 @@
           can be started up.
       err_event: We'll set this event in the case of an error (after printing
           out info about the error).
+
+    Returns:
+      Whether the fetch was successful.
     """
     # We'll set to true once we've locked the lock.
     did_lock = False
@@ -281,6 +300,8 @@
         lock.release()
       sem.release()
 
+    return success
+
   def _Fetch(self, projects, opt):
     fetched = set()
     pm = Progress('Fetching projects', len(projects))
@@ -303,20 +324,24 @@
           else:
             sys.exit(1)
     else:
+      objdir_project_map = dict()
+      for project in projects:
+        objdir_project_map.setdefault(project.objdir, []).append(project)
+
       threads = set()
       lock = _threading.Lock()
       sem = _threading.Semaphore(self.jobs)
       err_event = _threading.Event()
-      for project in projects:
+      for project_list in objdir_project_map.values():
         # Check for any errors before starting any new threads.
         # ...we'll let existing threads finish, though.
         if err_event.isSet():
           break
 
         sem.acquire()
-        t = _threading.Thread(target = self._FetchHelper,
+        t = _threading.Thread(target = self._FetchProjectList,
                               args = (opt,
-                                      project,
+                                      project_list,
                                       lock,
                                       fetched,
                                       pm,
@@ -342,6 +367,10 @@
     return fetched
 
   def _GCProjects(self, projects):
+    gitdirs = {}
+    for project in projects:
+      gitdirs[project.gitdir] = project.bare_git
+
     has_dash_c = git_require((1, 7, 2))
     if multiprocessing and has_dash_c:
       cpu_count = multiprocessing.cpu_count()
@@ -350,8 +379,8 @@
     jobs = min(self.jobs, cpu_count)
 
     if jobs < 2:
-      for project in projects:
-        project.bare_git.gc('--auto')
+      for bare_git in gitdirs.values():
+        bare_git.gc('--auto')
       return
 
     config = {'pack.threads': cpu_count / jobs if cpu_count > jobs else 1}
@@ -360,10 +389,10 @@
     sem = _threading.Semaphore(jobs)
     err_event = _threading.Event()
 
-    def GC(project):
+    def GC(bare_git):
       try:
         try:
-          project.bare_git.gc('--auto', config=config)
+          bare_git.gc('--auto', config=config)
         except GitError:
           err_event.set()
         except:
@@ -372,11 +401,11 @@
       finally:
         sem.release()
 
-    for project in projects:
+    for bare_git in gitdirs.values():
       if err_event.isSet():
         break
       sem.acquire()
-      t = _threading.Thread(target=GC, args=(project,))
+      t = _threading.Thread(target=GC, args=(bare_git,))
       t.daemon = True
       threads.add(t)
       t.start()
@@ -416,12 +445,13 @@
         if path not in new_project_paths:
           # If the path has already been deleted, we don't need to do it
           if os.path.exists(self.manifest.topdir + '/' + path):
+            gitdir = os.path.join(self.manifest.topdir, path, '.git')
             project = Project(
                            manifest = self.manifest,
                            name = path,
                            remote = RemoteSpec('origin'),
-                           gitdir = os.path.join(self.manifest.topdir,
-                                                 path, '.git'),
+                           gitdir = gitdir,
+                           objdir = gitdir,
                            worktree = os.path.join(self.manifest.topdir, path),
                            relpath = path,
                            revisionExpr = 'HEAD',
diff --git a/subcmds/upload.py b/subcmds/upload.py
index 8d801e0..9ad55d7 100644
--- a/subcmds/upload.py
+++ b/subcmds/upload.py
@@ -431,8 +431,10 @@
       hook = RepoHook('pre-upload', self.manifest.repo_hooks_project,
                       self.manifest.topdir, abort_if_user_denies=True)
       pending_proj_names = [project.name for (project, avail) in pending]
+      pending_worktrees = [project.worktree for (project, avail) in pending]
       try:
-        hook.Run(opt.allow_all_hooks, project_list=pending_proj_names)
+        hook.Run(opt.allow_all_hooks, project_list=pending_proj_names,
+                 worktree_list=pending_worktrees)
       except HookError as e:
         print("ERROR: %s" % str(e), file=sys.stderr)
         return