Split time_stepping.start into init, main_loop and finalize

I'd like to be able to modify the time_stepping parameters during a simulation.

We need to extend the API, since sim.time_stepping.start is responsible for

1. the initialization
2. the main time loop
3. closing files (by calling sim.__exit__)

I propose to add 2 new public methods:

• sim.time_stepping.main_loop
• sim.time_stepping.finalize_after_main_loop

Remarks/suggestions very welcome! (CC @avmo)