Gradle

Essentially in your Gradle build file you can specify a configuration like so

configurations {
    protoCompile
}

Then add the CLI dependency using that configuration.

dependencies {
    protoCompile "io.protostuff:protostuff-cli:0-SNAPSHOT"
}

Then to run it, just create task and do the following.

task generateSource() {
    ant.java(classname: 'io.protostuff.compiler.cli.ProtostuffCompilerCli', fork: 'true', failOnError: 'true') {
        arg(value: 'MyProto.proto')
        arg(value: '-g=java')
        arg(value: '-I=' + project.projectDir.path + "/../proto/")
        arg(value: '-o=' + project.buildDir.path + "/generated/")
        classpath {
            pathElement(path: configurations.protoCompile.asPath)
        }
    }
}

Then on call the task, I have it as part of the build so on "clean" the generated files are deleted and on build they are re-generated.

/gradlew generateSource

Thanks @MonsterOfCookie for instruction.