Added the start of a checkpoint file reporter. Currently, its also saving the serialized system/integrator, but I'm not sure if I like that. From the perspective of the python app, those actualyl ARENT enough to reinitialize the whole simulation, because it doesnt give enough data to attach the reporters. So instead, I think maybe the checkpoint file not claim to be itself sufficient to restart the simulation -- you need to provide the same config file and the topology... I'm not sure.
messing with the argparse loader
Removed IPython.application, since I was overriding it so much anyways.
merged in leepings work on master
minor changes