Syncs submodules after remote update (closes #370)

Previously, the Git code avoided cloning a local copy of the local
database for a repository if the repo already existed (and instead tried
to fetch). However, fetching does not sync and reinitialize submodules,
which would require more work.

To avoid this problem, and possibly other subtle updating issues in the
future, the code now wipes the local clone whenever it detects that the
HEAD of a particular branch has changed. This avoids subtle
inconsistencies between fresh clones and updates.

Note: This only affects local-to-local clones. It does not initiate any
new network activity. It may require some additional disk usage, but
only when a remote fetch that was already happening discovers new
commits on the checked-out branch.