add rule flag, closes #692

This is an initial attempt at this - please let me know if this is what you want.

I think this style - `--rule` merging with previous rules - is more useful than starting fresh with it, as it allows you to easily test out one small change to an existing config. If you want to start fresh you can simply use in combination with the `--reset` flag.

Also, is this using the `-r` alias OK, or should that be reserved for another flag?