If a subdir exists and is empty, go ahead and clone into it.

gclient_scm.py

 # 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.
 
 """Gclient-specific SCM-specific operations."""
 
 import logging
 import os
 import posixpath
 import re
@@ skipping 201 matching lines @@
     if revision.startswith('refs/heads/'):
       rev_type = "branch"
     elif revision.startswith('origin/'):
       # For compatability with old naming, translate 'origin' to 'refs/heads'
       revision = revision.replace('origin/', 'refs/heads/')
       rev_type = "branch"
     else:
       # hash is also a tag, only make a distinction at checkout
       rev_type = "hash"
 
-    if not os.path.exists(self.checkout_path):
+    if not os.path.exists(self.checkout_path) or (
+        os.path.isdir(self.checkout_path) and
+        not os.listdir(self.checkout_path)):
       gclient_utils.safe_makedirs(os.path.dirname(self.checkout_path))
       self._Clone(revision, url, options)
       files = self._Capture(['ls-files']).splitlines()
       file_list.extend([os.path.join(self.checkout_path, f) for f in files])
       if not verbose:
         # Make the output a little prettier. It's nice to have some whitespace
         # between projects when cloning.
         print('')
       return
 
@@ skipping 894 matching lines @@
       new_command.append('--force')
       if command[0] != 'checkout' and scm.SVN.AssertVersion('1.6')[0]:
         new_command.extend(('--accept', 'theirs-conflict'))
     elif options.manually_grab_svn_rev:
       new_command.append('--force')
       if command[0] != 'checkout' and scm.SVN.AssertVersion('1.6')[0]:
         new_command.extend(('--accept', 'postpone'))
     elif command[0] != 'checkout' and scm.SVN.AssertVersion('1.6')[0]:
       new_command.extend(('--accept', 'postpone'))
     return new_command