Refactor the CLI::Args module so it doesn't have different paths to
check arguments depending on whether the arguments have been parsed or
not. Instead, set the values we need from the global ARGV at
first, global initialisation time where they will be thrown away when
the actual arguments are parsed.

To do this some other general refactoring was needed:
- more methods made private when possible
- e.g. `HEAD?` used consistently instead of `head` before arguments
  are parsed.
- formula options are only parsed after named arguments are extracted