Fix CmdArgs module, to allow the args to be reparsed multiple times.

[mdsitton]

This makes the module a bit simpler to use cross engine overall since you dont have to track where the arguments are being parsed.

Basically the idea is to store all the values needed to pass into argparse, then when parse_args is called make a new instance of ArgumentParser and feed the arg options into it.

Some other cleanups are also needed, for example figure out how to get rid of the imo horrible syntax to get values out of the module. And maybe switch it to some kind of dictionary access type syntax

[mdsitton]

This will need to be implemented soon before my work on issue #16 approaches completion.