Avoid MVar deadlock issue, which I don't understand.
Have not taken the time to debug it fully, because it turns out I don't
need to resolve merge conflicts when a new branch ref is written... I
think.
Ensure the git-annex branch is merged when doing a manual pull.
Otherwise it can get out of sync, since git-annex normally only merges it
once per run.
SampleMVar won't work; between getting the current value and changing
it, another thread could made a change, which would get lost.
TMVar works well; this update situation is handled by atomic transactions.
