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By googling, I've stumbled upon Capt'n Proto, seems like it would do the trick. Does anyone have experience with using that?
You can certainly encode your individual messages with protobuf or Cap'n Proto and send them over your comms of choice, like ZeroMQ or RabbitMQ. Alternatively you could use an RPC mechanism that's heavily tied to the encoding, such as gRPC or Cap'n Proto's RPC. gRPC is widely used and I've found it excellent. It's based on Stubby which is used extensively in Google for their internal services.
Seconding protobufs and gRPC, they will most likely handle the data transfer. Bazel can seamlessly handle the dependencies. It's based on Google's internal build system.