Hm - this is a question of taste, of course. If run in standalone mode, we can either make each stage.py file     
 
  * write out a event map including everything up to this level
  * write out only the map/interaction that is generated at this level (e.g. the oscillation map)
  * ask for an input file from the previous stage and then apply this stage and write it out

In the spirit of keeping the code modular, I would think that we should not pick the first option, as it makes this stage dependent on the previous stage. Instead I would suggest to implement this part that:

  * if an input file from stage0 is provided, it is read in and the oscillations are applied to it
  * if no input file from stage0 is provided, it writes out just the oscillation maps by itself.