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

git_cl_hooks.py

Index: git_cl_hooks.py
===================================================================
--- git_cl_hooks.py	(revision 32839)
+++ git_cl_hooks.py	(working copy)
@@ -24,8 +24,11 @@
     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'])
@@ -37,7 +40,7 @@
     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)