Don't delete directories that have been superseded by a broader checkout.

gclient_scm.py

Index: gclient_scm.py
diff --git a/gclient_scm.py b/gclient_scm.py
index ba49f050c66d4a41a416dd801af2247e4ff32223..01dfd54675b32151d38eb6fe27629650397a32bd 100644
--- a/gclient_scm.py
+++ b/gclient_scm.py
@@ -173,6 +173,9 @@ class GitWrapper(SCMWrapper):
     except OSError:
       return False
 
+  def GetCheckoutRoot(self):
+    return scm.GIT.GetCheckoutRoot(self.checkout_path)
+
   def GetRevisionDate(self, revision):
     """Returns the given revision's date in ISO-8601 format (which contains the
     time zone)."""
@@ -920,6 +923,9 @@ class SVNWrapper(SCMWrapper):
     except OSError:
       return False
 
+  def GetCheckoutRoot(self):
+    return scm.SVN.GetCheckoutRoot(self.checkout_path)
+
   def GetRevisionDate(self, revision):
     """Returns the given revision's date in ISO-8601 format (which contains the
     time zone)."""