[JobQueue] Throttle refreshLinks2 jobs based on finishing the refreshLinks jobs.

* This should lower the rate of queue activity when major templates change.
* Also fixed a broken array_diff() call in nextJobDB.php.
* Additionally removed checkJob from nextJobDB.php. This is redundant to
  runJobs.php de-listing queues via JobQueueGroup::pop() when the queue
  is empty.

Change-Id: I1518a0de9e7ada22350d9993dd7ffe5f2ce23745