in_directory was not being set to the correct cwd. This caused commands to
always run in the dir from which gclient was executed.
Review URL: http://codereview.chromium.org/554142
git-svn-id: svn://svn.chromium.org/chrome/trunk/tools/depot_tools@37697 0039d316-1c4b-4281-b951-d872f2087c98