deprecate SimulationOutput

[nkrah]

There is actually no need anymore for the SimulationOutput class. It would be simpler to pass back the Simulation object from a subprocess and do all merging operations based on that. This would also pave the road for remote multiprocessing where the one Simulation object per process could be recreated from the json file.

Background: The SimulationOutput was necessary before the engines were restructured, before pickling was properly implemented, and before the actors were refactored. It has now actually become redundant. We might need to check if the sources need to be refactored into GateObjects first to fully avoid the SimulationOutput object.