Refactor subcommand methods to use named args (too long method signature)

[ptrpfn]

via @jwaggs in PR 109 and 110:

our subcommands are getting pretty bloated - it will likely be worth it to refactor them into better bite sized chunks at some point. But until then, it might be good to use keyword args instead of positional args. In general if there are more than 2 or 3 parameters I like to shift to using keyword args.

Example from commands.py:

def verify_entire_folder(
    root_path, verbose, packing_list_path, ignore_list=None, ignore_spec_file=None, calculate_only=None
):