Issue/normalize args

Addresses #279, and starts to address #252. Will address #252 before merge.

#117 is addressed implicitly for any scripts using these functions (which should be all...)

[x] Unify and standardize argument parsing
[x] Update scripts to use standardized arg parsing
[ ] Add a function pull ksize, nhashes, and hashsize from saved hash
[ ] Add standardized checkpointing args (#252)