buildscript {
  repositories {
    mavenCentral()
  }
  dependencies {
    classpath 'com.google.protobuf:protobuf-gradle-plugin:0.8.10'
  }
}

plugins {
  ...
  id 'com.google.protobuf' version "0.8.10"
}
...
sourceSets {
  main {
    java {
      srcDir 'src/main/protoGen'
    }
  }
}

protobuf {
  ...
  generateProtoTasks {
    ofSourceSet('main').each { task ->
      task.builtins {
        java {
          outputSubDir = 'protoGen'
        }
      }
      task.plugins {
        grpc {
          outputSubDir = 'protoGen'
        }
      }
    }
  }
  generatedFilesBaseDir = "$projectDir/src/"
}
...