Prototype checkpoint implementation #80

Also turned off logging when running unit tests
Put in temp file deleting code for #88 and fixed some bugs
More comments for checkpointing, fixed small bug #88

Unit tests pass
Turned off some logging, option to keep temp files, tests #88¬
Put in regression tests, fixed small bugs, improved exceptions #88
Removed ability to specify temp files in inputs #88
Added checkpoints testing to run-all regtest script #88