Building a Kotlin + Java 9 project with Gradle

I am using the following gradle script where I put the module-info.java under src/module. It gets automatically included in the jar (without duplicates):

if (JavaVersion.current() >= JavaVersion.VERSION_1_9) {
    subprojects {
        def srcModule = "src/module"
        def moduleInfo = file("${project.projectDir}/$srcModule/module-info.java")
        if (moduleInfo.exists()) {

            sourceSets {
                module {
                    java {
                        srcDirs = [srcModule]
                        compileClasspath = main.compileClasspath
                        sourceCompatibility = '9'
                        targetCompatibility = '9'
                    }
                }
                main {
                    kotlin { srcDirs += [srcModule] }
                }
            }

            compileModuleJava.configure {
                dependsOn compileKotlin
                destinationDir = compileKotlin.destinationDir
                doFirst {
                    options.compilerArgs = ['--module-path', classpath.asPath,]
                    classpath = files()
                }
            }
            jar.dependsOn compileModuleJava
        }
    }
}

I won't update it any longer, have a look at https://github.com/robstoll/atrium/blob/master/build.gradle to see the current version in use.

Solved! It was sufficient to set the kotlin compilation dir to the same dir as Java:

compileKotlin.destinationDir = compileJava.destinationDir

It works now, both with the sources in the same tree or in different trees; but with a quirk: the jar task produces a jar with all the entries duplicated. I'll work on fix this, next.

Thanks to everyone!

The accepted answer did not work for me (atleast not the way it was presented), but this is what worked:

plugins {
    id "org.jetbrains.kotlin.jvm" version "1.3.50"
}

compileKotlin {
    doFirst {
        destinationDir = compileJava.destinationDir
    }
}

jar {
    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
}

Doing it the way the accepted answer suggests led to me getting this error:

Directory '/path/to/project/build/classes/kotlin/main' specified for property 'compileKotlinOutputClasses' does not exist.

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Gradle version: 5.6