In a multiproject Gradle build with potentially empty intermediate directories, here is how to avoid empty build/ directories. Only apply the java plugin to directories containing actual source.

omitemptybuild.gradle

afterEvaluate { project ->
    configure(subprojects.findAll { new File(it.projectDir, "src").exists() }) {
        apply plugin: 'java'
        compileJava {
            options.compilerArgs << '-Xlint:unchecked'
        }

        sourceCompatibility = targetCompatibility = 1.6

        tasks.withType(Test) {
            systemProperties = System.getProperties()
            jvmArgs '-Xmx1g'
            testLogging {
                showStandardStreams = true
                exceptionFormat "full"
                events "failed", "standardOut", "standardError"
            }
        }

        tasks.withType(Compile) {
            options.encoding = 'UTF-8'
        }
    }

}