Clean up SimulationGenerator

Fix: Remove some unnecessary method parameters from SimulationGenerator.
World keeps reference to Simulation during persistence

Fix: The World object keeps its reference to the Simulation object it is used in after a serialization/deserialization of the simulation.
General javadoc fixes

Fix: Some more small javadoc issues.
Clean up starting process in Main

Fix: Clean up the part of the Main class that starts up the game.