Spurious Joshua timeout in shared environment

We observed that running in a shared environment (e.g., docker and AWS spot instances), the correctness runs of Joshua results are often `timeout` errors. These errors can become very noisy if the CPU resources on the test machine is heavily contended. So it would be very useful we can filter them out.

One idea I have is for `TestHarness` to check the progress of simulation runs. Rerun the simulation for `timeout` errors.

Locate TestHarness and the Joshua correctness-run handling; first inspect how simulation progress and timeout errors are reported. Done means timeout results caused by shared-resource contention are handled by rerunning the simulation, with coverage for that behavior.

Written by the indexing model from the issue text.