Convert JobRunner to using beginMasterChanges()

Convert JobRunner to using beginMasterChanges()

This lets the runJobs.php $wgCommandLineMode hack be removed.

Some fixes based on unit tests:
* Only call applyTransactionRoundFlags() for master connections
  for transaction rounds from beginMasterChanges().
* Also cleaned up the commitAndWaitForReplication() reset logic.
* Removed deprecated DataUpdate::doUpdate() calls from jobs
  since they cannot nest in a transaction round.

Change-Id: Ia9b91f539dc11a5c05bdac4bcd99d6615c4dc48d