[Tools] Unbreak fetch_deps.py after Chromium r249077.

depot_tools commit 249077 broke our fetch_deps.py because gclient does not
accept absolute paths in --gclient-file anymore.

Since we already set cwd when calling
gclient_utils.CheckCallAndFilterAndHeader(), we can just strip the rest of
the path in self._new_gclient_file to fix things.

BUG=https://crosswalk-project.org/jira/browse/XWALK-930
Merge pull request #1560 from rakuco/fetch-deps-new-depot_tools

[Tools] Unbreak fetch_deps.py after Chromium r249077.