Don't delete directories that have been superseded by a broader checkout.

gclient.py

 #!/usr/bin/env python
 # Copyright (c) 2012 The Chromium Authors. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 
 """Meta checkout manager supporting both Subversion and GIT.
 
 Files
   .gclient      : Current client configuration, written by 'config' command.
                   Format is a Python script defining 'solutions', a list whose
@@ skipping 1116 matching lines @@
     # Once all the dependencies have been processed, it's now safe to run the
     # hooks.
     if not self._options.nohooks:
       self.RunHooksRecursively(self._options)
 
     if command == 'update':
       # Notify the user if there is an orphaned entry in their working copy.
       # Only delete the directory if there are no changes in it, and
       # delete_unversioned_trees is set to true.
       entries = [i.name for i in self.root.subtree(False) if i.url]
+      full_entries = [os.path.join(self.root_dir, e.replace('/', os.path.sep))
+                      for e in entries]
+
       for entry, prev_url in self._ReadEntries().iteritems():
         if not prev_url:
           # entry must have been overridden via .gclient custom_deps
           continue
         # Fix path separator on Windows.
         entry_fixed = entry.replace('/', os.path.sep)
         e_dir = os.path.join(self.root_dir, entry_fixed)
 
         def _IsParentOfAny(parent, path_list):
           parent_plus_slash = parent + '/'
           return any(
               path[:len(parent_plus_slash)] == parent_plus_slash
               for path in path_list)
 
         # Use entry and not entry_fixed there.
         if (entry not in entries and
             (not any(path.startswith(entry + '/') for path in entries)) and
             os.path.exists(e_dir)):
+          scm = gclient_scm.CreateSCM(prev_url, self.root_dir, entry_fixed)
+
+          # Check to see if this directory is now part of a higher-up checkout.
+          if scm.GetCheckoutRoot() in full_entries:
+            logging.info('%s is part of a higher level checkout, not '
+                         'removing.', scm.GetCheckoutRoot())
+            continue
+
           file_list = []
-          scm = gclient_scm.CreateSCM(prev_url, self.root_dir, entry_fixed)
           scm.status(self._options, [], file_list)
           modified_files = file_list != []
           if (not self._options.delete_unversioned_trees or
               (modified_files and not self._options.force)):
             # There are modified files in this entry. Keep warning until
             # removed.
             print(('\nWARNING: \'%s\' is no longer part of this client.  '
                    'It is recommended that you manually remove it.\n') %
                       entry_fixed)
           else:
@@ skipping 622 matching lines @@
   except (gclient_utils.Error, subprocess2.CalledProcessError), e:
     print >> sys.stderr, 'Error: %s' % str(e)
     return 1
 
 
 if '__main__' == __name__:
   fix_encoding.fix_encoding()
   sys.exit(Main(sys.argv[1:]))
 
 # vim: ts=2:sw=2:tw=80:et: