Use end-to-end simulation capabilities in FLFLL

[wlandau-lilly]

Prework

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Proposal

The new FLFLL has the ability to run simulations. This could potentially simplify run_facts() and make it easier to maintain. Might also simplify system configuration.

[wlandau-lilly]

I would have if I had started developing on top of FLFLL >= 6.4.1, but at this stage it does not seem to be worth it.