Removed most references to FreeMovingBodies

Attempting to simplify the logic by tracking the bodies in a single list
and adding special cases for the black spheres.
Added function to return the body that is removed
Implemented toBeRemoved; removed some old code
Added flag to check for dead bodies; fcn to remove them

Changed record function to mark the body as dead instead of deleting it
Changed to mark bodies as dead instead of deleting in place
Renamed fucntion to better represent functionality
Changed function name