diff --git a/main.py b/main.py
index 47f083d..6736abc 100755
--- a/main.py
+++ b/main.py
@@ -45,6 +45,7 @@
 from subcmds.version import Version
 from editor import Editor
 from error import DownloadError
+from error import InvalidProjectGroupsError
 from error import ManifestInvalidRevisionError
 from error import ManifestParseError
 from error import NoManifestException
@@ -173,6 +174,12 @@
       else:
         print('error: no project in current directory', file=sys.stderr)
       result = 1
+    except InvalidProjectGroupsError as e:
+      if e.name:
+        print('error: project group must be enabled for project %s' % e.name, file=sys.stderr)
+      else:
+        print('error: project group must be enabled for the project in the current directory', file=sys.stderr)
+      result = 1
     finally:
       elapsed = time.time() - start
       hours, remainder = divmod(elapsed, 3600)
diff --git a/manifest_xml.py b/manifest_xml.py
index cfbd9ef..130e17c 100644
--- a/manifest_xml.py
+++ b/manifest_xml.py
@@ -253,11 +253,13 @@
         else:
           value = p.work_git.rev_parse(HEAD + '^0')
         e.setAttribute('revision', value)
-        if peg_rev_upstream and value != p.revisionExpr:
-          # Only save the origin if the origin is not a sha1, and the default
-          # isn't our value, and the if the default doesn't already have that
-          # covered.
-          e.setAttribute('upstream', p.revisionExpr)
+        if peg_rev_upstream:
+          if p.upstream:
+            e.setAttribute('upstream', p.upstream)
+          elif value != p.revisionExpr:
+            # Only save the origin if the origin is not a sha1, and the default
+            # isn't our value
+            e.setAttribute('upstream', p.revisionExpr)
       else:
         revision = self.remotes[remoteName].revision or d.revisionExpr
         if not revision or revision != p.revisionExpr:
diff --git a/project.py b/project.py
index 3f1e3b6..00f6b90 100644
--- a/project.py
+++ b/project.py
@@ -544,6 +544,12 @@
 
 
 class Project(object):
+  # These objects can be shared between several working trees.
+  shareable_files = ['description', 'info']
+  shareable_dirs = ['hooks', 'objects', 'rr-cache', 'svn']
+  # These objects can only be used by a single working tree.
+  working_tree_files = ['config', 'packed-refs', 'shallow']
+  working_tree_dirs = ['logs', 'refs']
   def __init__(self,
                manifest,
                name,
@@ -645,7 +651,7 @@
 
   @property
   def Exists(self):
-    return os.path.isdir(self.gitdir)
+    return os.path.isdir(self.gitdir) and os.path.isdir(self.objdir)
 
   @property
   def CurrentBranch(self):
@@ -1131,7 +1137,6 @@
               "%s" % (tarpath, str(e)), file=sys.stderr)
       self._CopyAndLinkFiles()
       return True
-
     if is_new is None:
       is_new = not self.Exists
     if is_new:
@@ -1876,8 +1881,6 @@
       cmd.append('--quiet')
     if not self.worktree:
       cmd.append('--update-head-ok')
-    if self.manifest.IsMirror:
-      cmd.append('--prune')
     cmd.append(name)
 
     # If using depth then we should not get all the tags since they may
@@ -1897,7 +1900,7 @@
 
     if not self.manifest.IsMirror:
       branch = self.revisionExpr
-      if is_sha1 and depth:
+      if is_sha1 and depth and git_require((1, 8, 3)):
         # Shallow checkout of a specific commit, fetch from that commit and not
         # the heads only as the commit might be deeper in the history.
         spec.append(branch)
@@ -1960,8 +1963,15 @@
       # got what we wanted, else trigger a second run of all
       # refs.
       if not self._CheckForSha1():
-        return self._RemoteFetch(name=name, current_branch_only=False,
-                                 initial=False, quiet=quiet, alt_dir=alt_dir)
+        if not depth:
+          # Avoid infinite recursion when depth is True (since depth implies
+          # current_branch_only)
+          return self._RemoteFetch(name=name, current_branch_only=False,
+                                   initial=False, quiet=quiet, alt_dir=alt_dir)
+        if self.clone_depth:
+          self.clone_depth = None
+          return self._RemoteFetch(name=name, current_branch_only=current_branch_only,
+                                   initial=False, quiet=quiet, alt_dir=alt_dir)
 
     return ok
 
@@ -2155,19 +2165,24 @@
       raise GitError('%s merge %s ' % (self.name, head))
 
   def _InitGitDir(self, mirror_git=None):
-    if not os.path.exists(self.gitdir):
+    init_git_dir = not os.path.exists(self.gitdir)
+    init_obj_dir = not os.path.exists(self.objdir)
+    # Initialize the bare repository, which contains all of the objects.
+    if init_obj_dir:
+      os.makedirs(self.objdir)
+      self.bare_objdir.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:
+    # If we have a separate directory to hold refs, initialize it as well.
+    if self.objdir != self.gitdir:
+      if init_git_dir:
         os.makedirs(self.gitdir)
+
+      if init_obj_dir or init_git_dir:
         self._ReferenceGitDir(self.objdir, self.gitdir, share_refs=False,
                               copy_all=True)
+      self._CheckDirReference(self.objdir, self.gitdir, share_refs=False)
 
+    if init_git_dir:
       mp = self.manifest.manifestProject
       ref_dir = mp.config.GetString('repo.reference') or ''
 
@@ -2273,6 +2288,21 @@
         msg = 'manifest set to %s' % self.revisionExpr
         self.bare_git.symbolic_ref('-m', msg, ref, dst)
 
+  def _CheckDirReference(self, srcdir, destdir, share_refs):
+    symlink_files = self.shareable_files
+    symlink_dirs = self.shareable_dirs
+    if share_refs:
+      symlink_files += self.working_tree_files
+      symlink_dirs += self.working_tree_dirs
+    to_symlink = symlink_files + symlink_dirs
+    for name in set(to_symlink):
+      dst = os.path.realpath(os.path.join(destdir, name))
+      if os.path.lexists(dst):
+        src = os.path.realpath(os.path.join(srcdir, name))
+        # Fail if the links are pointing to the wrong place
+        if src != dst:
+          raise GitError('cannot overwrite a local work tree')
+
   def _ReferenceGitDir(self, gitdir, dotgit, share_refs, copy_all):
     """Update |dotgit| to reference |gitdir|, using symlinks where possible.
 
@@ -2284,13 +2314,11 @@
       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']
+    symlink_files = self.shareable_files
+    symlink_dirs = self.shareable_dirs
     if share_refs:
-      # These objects can only be used by a single working tree.
-      symlink_files += ['config', 'packed-refs', 'shallow']
-      symlink_dirs += ['logs', 'refs']
+      symlink_files += self.working_tree_files
+      symlink_dirs += self.working_tree_dirs
     to_symlink = symlink_files + symlink_dirs
 
     to_copy = []
@@ -2302,8 +2330,8 @@
         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 os.path.lexists(dst):
+          continue
 
         # If the source dir doesn't exist, create an empty dir.
         if name in symlink_dirs and not os.path.lexists(src):
@@ -2332,11 +2360,15 @@
 
   def _InitWorkTree(self):
     dotgit = os.path.join(self.worktree, '.git')
-    if not os.path.exists(dotgit):
+    init_dotgit = not os.path.exists(dotgit)
+    if init_dotgit:
       os.makedirs(dotgit)
       self._ReferenceGitDir(self.gitdir, dotgit, share_refs=True,
                             copy_all=False)
 
+    self._CheckDirReference(self.gitdir, dotgit, share_refs=True)
+
+    if init_dotgit:
       _lwrite(os.path.join(dotgit, HEAD), '%s\n' % self.GetRevisionId())
 
       cmd = ['read-tree', '--reset', '-u']
diff --git a/subcmds/forall.py b/subcmds/forall.py
index ebc8bec..b93cd6d 100644
--- a/subcmds/forall.py
+++ b/subcmds/forall.py
@@ -151,11 +151,15 @@
     attributes that we need.
 
     """
+    if not self.manifest.IsMirror:
+      lrev = project.GetRevisionId()
+    else:
+      lrev = None
     return {
       'name': project.name,
       'relpath': project.relpath,
       'remote_name': project.remote.name,
-      'lrev': project.GetRevisionId(),
+      'lrev': lrev,
       'rrev': project.revisionExpr,
       'annotations': dict((a.name, a.value) for a in project.annotations),
       'gitdir': project.gitdir,
@@ -201,6 +205,13 @@
     mirror = self.manifest.IsMirror
     rc = 0
 
+    smart_sync_manifest_name = "smart_sync_override.xml"
+    smart_sync_manifest_path = os.path.join(
+      self.manifest.manifestProject.worktree, smart_sync_manifest_name)
+
+    if os.path.isfile(smart_sync_manifest_path):
+      self.manifest.Override(smart_sync_manifest_path)
+
     if not opt.regex:
       projects = self.GetProjects(args)
     else:
diff --git a/subcmds/sync.py b/subcmds/sync.py
index b4546c1..ec333ae 100644
--- a/subcmds/sync.py
+++ b/subcmds/sync.py
@@ -517,6 +517,9 @@
       self.manifest.Override(opt.manifest_name)
 
     manifest_name = opt.manifest_name
+    smart_sync_manifest_name = "smart_sync_override.xml"
+    smart_sync_manifest_path = os.path.join(
+      self.manifest.manifestProject.worktree, smart_sync_manifest_name)
 
     if opt.smart_sync or opt.smart_tag:
       if not self.manifest.manifest_server:
@@ -583,17 +586,16 @@
           [success, manifest_str] = server.GetManifest(opt.smart_tag)
 
         if success:
-          manifest_name = "smart_sync_override.xml"
-          manifest_path = os.path.join(self.manifest.manifestProject.worktree,
-                                       manifest_name)
+          manifest_name = smart_sync_manifest_name
           try:
-            f = open(manifest_path, 'w')
+            f = open(smart_sync_manifest_path, 'w')
             try:
               f.write(manifest_str)
             finally:
               f.close()
-          except IOError:
-            print('error: cannot write manifest to %s' % manifest_path,
+          except IOError as e:
+            print('error: cannot write manifest to %s:\n%s'
+                  % (smart_sync_manifest_path, e),
                   file=sys.stderr)
             sys.exit(1)
           self._ReloadManifest(manifest_name)
@@ -610,6 +612,13 @@
               % (self.manifest.manifest_server, e.errcode, e.errmsg),
               file=sys.stderr)
         sys.exit(1)
+    else:  # Not smart sync or smart tag mode
+      if os.path.isfile(smart_sync_manifest_path):
+        try:
+          os.remove(smart_sync_manifest_path)
+        except OSError as e:
+          print('error: failed to remove existing smart sync override manifest: %s' %
+                e, file=sys.stderr)
 
     rp = self.manifest.repoProject
     rp.PreSync()