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Use a single global value for the current runtime, this should avoid issues with the exact timing of when the limit is exceeded

Backport a fix from the COLIBRE repo to solve a segfault in the cleaning routines when ending a run that restarted from check-point files.

This reverts merge request !839

A better catch all solution is to track if stf has been run this timestep,
e->stf_this_timestep, and only invoke velociraptor is this value is 0.

Only call engine_rebuild() and not engine_init_particles() in main_fof. We don't need the full thing.

Changed the way we set the run frequency to use a physical simulation time rather than a fixed number of steps.

add a new engine_step_prop_stop which makes the runners quit if set. engine_clean now sets the prop, releases the runners, and pthread_waits on them.

Created function to run FOF search. Run FOF before a rebuild and not when a repartition is scheduled.