Fix GetCachedFile() to skip local mods when use_root is True. The files
that exist in the root of the tree don't even seem to exist in the normal
source checkouts, and we were looking at a different file as a result.

  BUG=none
  R=maruel@chromium.org
  TEST=locally modify a PRESUBMIT.py file and look for duplicate results. 
    If you get duplicates, this didn't fix it

Review URL: http://codereview.chromium.org/379021

git-svn-id: svn://svn.chromium.org/chrome/trunk/tools/depot_tools@31586 0039d316-1c4b-4281-b951-d872f2087c98