Check out [StartupExampleDummy.java](https://github.com/jTendermint/jabci/blob/master/src/main/java/com/github/jtendermint/jabci/StartupExampleDummy.java) or [JavaCounter.java](https://github.com/jTendermint/jabci/blob/master/src/main/java/com/github/jtendermint/jabci/JavaCounter.java) for examples.
When you make changes to the protobuf file, you can enable the appropriate build-phase for the compiler-plugin to generate the file(s) in the target-directory.