Use git clean -ffd to reset repos after switching branches

This will remove any submodules that were initalized but don't
exist in older branches, like lib/ve in VisualEditor.

We need to use a second f since the repo is tracked by git, and
would be skipped by a normal "-fd".

Change-Id: Ibd89d825a9c7220c0db861c9e40b60fcda564d4c