When my binary sends an UDP packet to the provided test binary via the Gossip Port, the test binary prints "ERROR: empty protobuf packet". The JSON that I send is non-empty.
Unless you add debug statements *in your own code*, and share them here, we're unlikely to be able to help. What test are you running, what exactly does your gossiper send, from which address?
I saw that there is a protobuf library on github.com/dedis/protobuf. Should we use this or JSON?
Certainly not. JSON is the expected encoding, just as the handouts specify.