Don't delete directories that have been superseded by a broader checkout.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 9ccc76f217059810e41f3fd66e30affd7ff4727e..0d30460ba81a272341bec24b6a33a76d8706037b 100644
--- a/gclient_scm.py
+++ b/gclient_scm.py
@@ -169,6 +169,9 @@ 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)."""
@@ -910,6 +913,9 @@ 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)."""