Refactoring to engine and entrypoint script

Refactor main.py and multi-part-sim.py logic into reusable functions. The simulation setup logic is now in Engine.from_sim_config, and MultiPartEngine.from_sim_config. I'll use these methods in the simulation server to run the simulation and get the results programmatically. These can also be helpful for the tests as we can check the actual results of the simulation.

Remove multi-part-sim.py and combine everything into a single entrypoint script that you can use subcommands on, e.g. python main.py run ..., python main.py run-multi-part ....

Also register main.py as a script so that now after installing the project (python -m pip install -e .) it should be available as just raps.

This has broken the mpi version of the multi-partition run so I've just removed it. We can add that back later.