I have submitted two changes for review that hopefully remedy the current 
problems:

* I1e746322 implements better documentation, more consistent behavior, and
easier tracking of implicit commits in Database::begin()

* I6ecb8faa restores the "flushing" commits that I removed a while ago under the
assumption that a commit without a begin would be a no-op.

I hope this addresses any pressing issues.

I still think that we need a way to protect critical sections. But an RFC seems
to be in order for that.

-- daniel

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