Add/use 1 step Simulation.update method

PHYS-16 #time 15m
Move unused parallelization bit to init function

PHYS-16 #time 5m
Consolidate more Sim update code into class

PHYS-16 #time 10m
Fix catastrophic error in calcForcesAll

PHYS-16 #time 30m

I finally noticed that I had eliminated the line that gave object2 an
active Shape to work with, so it was always null. I'm VERY confused as
to how I could have gone so far last night without encountering this
error.
Simplify some interaction loops

PHYS-16 #time 10m