Better CLI

Currently we just use a lot of

if "command" in sys.argv:
    sys.argv[sys.argv.index(command) + 1]

... to parse the cli flags but this seems to be a little inefficient and hard to maintain. Something better such as a separate module would be better. And, we need a more robust and flexible command line so that you don't need to edit the config.py file for a temporary change.