InitGitDir: Clean up created directories

If _InitGitDir fails, it leaves any progress it had made on the file
system. This can cause subsequent calls to repo sync to behave
differently. This is especially evident when _CheckDirReference() fails,
since it will not be invoked when sync is retried because both the
source and destination directories already exist.

To address this, have _InitGitDir() clean up any directories it has created
if it catches an exception. Also behave the same way for _InitWorkTree().

Change-Id: Ic16bb3feea649e115b59bd44be294e89e3692aeb