Database transaction flushing cleanups

Database transaction flushing cleanups

* Do not commit() inside masterPosWait(). This could happen
  inside JobRunner::commitMasterChanges, resulting in
  one DB committing while the others may or may not later commit.
* Migrate some commit() callers to commitMasterChanges().
* Removed unsafe upload class commit() which could break
  outer transactions.
* Also cleaned up the "flush" flag to make it harder to misuse.

Change-Id: I75193baaed979100c5338abe0c0899abba3444cb