Make USB communication use protobuf to pass messages between remote and target

[dNechita]

Currently, a remote application sends/receives messages over USB (using the UVC and its extension unit) in a format that is custom made. And it is not even consistent for all messages. For instance, sending the firmware to the target is done differently than sending a bunch of AFE registers to be written. We should use protobuf to encode the messages that we want to send/receive.