refactor(pb) move protos to internal packages

Omitted `handshake` because it's addressed on https://github.com/jbenet/go-ipfs/tree/dhtfixes

Omitted `dht` because there's a decision to be made about message.go. To move routing/dht/Message.go into the `pb` package with the protos, would need to remove the logging statement shown below. If y'all are cool with this, I'll go ahead and make the change. I'm reluctant to make functional changes for the sake of style. Hence, the omission.

https://github.com/jbenet/go-ipfs/blob/fix/move_proto/routing/dht/Message.go#L56

re internal packages:
https://docs.google.com/document/d/1e8kOo3r51b2BWtTs_1uADIA5djfXhPT36s6eHVRIvaU/edit
General Makefile