Fix argparse bugs

Fixes #172

* Fixed a bug in which the version was retrieved twice, raising a `KeyError`. `argparse` does it automatically with `action=version`, without creating any `version` key in the `args` dictionary.
* Fixed a bug when returning the parsed arguments in `parse_arguments()`
* The arguments are now accessed properly
* Added a `command` positional argument


TODO (I will coordinate this with @thekorn, as he knows more about how the current argument parsing works)
- Retrieve the `command` argument
- We can probably clean up the argument parsing a bit more, relying on `argparse`'s power