Use subclasses and imports rather than vendoring protocols

[IAlibay]

Please see here: #1 (comment)

The protocols are still being worked on upstream and they are being designed to be subclassed. Vendoring here is only going to lead to extra work & headaches.

TLDR; I spent a lot of time making sure that you could minimally create subclasses of the AFE protocol which only changed things like how you parameterize things. The same thing is WIP for the MD and RFE protocols.