Call git diff --name-status with a relative path....

git_cl_hooks.py

 # Copyright (c) 2009 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.
 
 import os
 import re
 import subprocess
 import sys
 
 import presubmit_support
 import scm
 
 def Backquote(cmd, cwd=None):
   """Like running `cmd` in a shell script."""
   return subprocess.Popen(cmd,
                           cwd=cwd,
                           stdout=subprocess.PIPE).communicate()[0].strip()
 
 
 class ChangeOptions:
   def __init__(self, commit=None, upstream_branch=None):
     self.commit = commit
     self.verbose = None
     self.default_presubmit = None
     self.may_prompt = None
 
-    root = os.path.abspath(Backquote(['git', 'rev-parse', '--show-cdup']))
+    root = Backquote(['git', 'rev-parse', '--show-cdup'])
+    if not root:
+      root = "."
+    absroot = os.path.abspath(root)
     if not root:
       raise Exception("Could not get root directory.")
     log = Backquote(['git', 'show', '--name-only',
                      '--pretty=format:%H%n%s%n%n%b'])
     m = re.match(r'^(\w+)\n(.*)$', log, re.MULTILINE|re.DOTALL)
     if not m:
       raise Exception("Could not parse log message: %s" % log)
     name = m.group(1)
     description = m.group(2)
     files = scm.GIT.CaptureStatus([root], upstream_branch)
     issue = Backquote(['git', 'cl', 'status', '--field=id'])
     patchset = None
-    self.change = presubmit_support.GitChange(name, description, root, files,
+    self.change = presubmit_support.GitChange(name, description, absroot, files,
                                               issue, patchset)
 
 
 def RunHooks(hook_name, upstream_branch):
   commit = (hook_name == 'pre-cl-dcommit')
 
   # Create our options based on the command-line args and the current checkout.
   options = ChangeOptions(commit=commit, upstream_branch=upstream_branch)
 
   # Run the presubmit checks.
   if presubmit_support.DoPresubmitChecks(options.change,
                                          options.commit,
                                          options.verbose,
                                          sys.stdout,
                                          sys.stdin,
                                          options.default_presubmit,
                                          options.may_prompt):
     sys.exit(0)
   else:
     sys.exit(1)