Correctly determine working copy root when inside submodule.

This fixes error messages like "fatal: '/path/to/file' is outside repository" when using the bundle with git submodules.

`Git.path` assumed that the git dir would always be located directly below the working copy root. However, this is not (no longer?) true when working with submodules: The git dir of a submodule is nested inside the parent project’s git dir.

Using `git rev-parse --show-toplevel` (available since Git 1.7.0) figures this out correctly, even for submodules.

Similar incorrect code existed in `Compare Branches.tmCommand`. This was dead code however (`path` not being used anywhere afterwards), so I removed the line there completely.