Added timeouts/timing debug to ctrlr.

The timeouts should now be run in a separate daemon thread.
They have a granularity of 5 seconds, which we might be able to
bring down, but I don't want any weird errors during our early
evaluation.

Some timing code has been added also. It will log to a file after
shutting down; telling how long operations took. It will need
to close via a normal DSM path to do this though.