Disambiguate options and commands

As I am refactoring the command-line flag handling code, I have noticed that many commands have "options" which fundamentally change the mode (operation) of the command. For example, consider the `register` command; it has three separate modes and two of them don't actually register the package! This is probably confusing to the user and it's certainly messier to implement.

I propose splitting all the "modes" out into their own commands, so that all the "options" are actually options. I think Cabal 2.0 is the ideal time to introduce such changes that break command-line compatibility.