Alex Lin fa4664c4ea Move the loop that waits for scheduled threads to finish out of advance_sim_time #292
2 problems found.  Syncing scheduled threads was not happening at all because the job
was not being rescheduled.  Did not want to deal with changing job call times so I
called the new scheuduled_thread_sync routine from advance_sim_time.  That's where
it started, it'll be fine.

Also found that I was resetting job complete flags too aggressively.  The check to
test if the thread is ready to run was missing.  Added that check back in.
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..
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