Recreated initial set files

Recreated the initial gen-0 set files where the old triangle
restrictions no longer apply and the stable sets are the same across
all chains/conditions.
No longer produce stable set files

Now that we have one stable set file for all chains and conditions, we
no longer need to randomly generate these when creating the initial
gen-0 set files.
General clean up

General clean up of the code after yesterday's overhaul