Update the `CroState` to make molecules accessable individually

[Saethox]

The components updating the CroState currently need to juggle with indices to avoid borrowing two Molecules mutably at the same time, so we might want to look into replacing Vec with something that allows multiple mutable references to distinct indices. The current solution works, but is pretty unreadable.

[Saethox]

I found this gives more troubles than benefits, as the index is needed for the population anyway.