Allow running without outputting stage 2 simulation data.

[a-t-0]

• [x] Include CLI arg to prevent outputting stage 2 simulation data.
• [x] In stage 2, include a check for each graph whether the results for that graph already exist. If yes, then don't simulate, nor load it.
• [x] Ensure results can be computed directly from the simulation.
• [x] Verify this works by first generating the results completely, and then deleting the stage2 data and verifying that everything works.

[a-t-0]

Done.