First, using a single classes directory (setting
sourceSets.main.output.classesDir
) is considered deprecated since Gradle 4.0, the builds should support separate classes directories for the JVM languages (the file collection is
sourceSets.main.output.classesDirs
).
As to the destination directory that Kotlin uses, you can set it with
compileKotlin.destinationDir = ...
.
Though the fact that
sourceSets.main.kotlin.outputDir = ...
doesn't work seems to be a bug, I'll check it.