Right now we tell our users to add this snippet to their project if they want to use annotation processors:

configurations {
  apt
}

tasks.withType(JavaCompile) {
  options.annotationProcessorPath = configurations.apt
}

This should work out of the box and each SourceSet should have an annotationProcessor configuration. For backwards compatibility we can do what the Android team did: Emit a deprecation warning when we find annotation processors on the compileClasspath (and add it to the annotation processor path to keep the build running) and add a flag to CompileOptions to allow the user to ignore these processors. We can then turn that warning into a failure in the next major release and deprecate the flag, because its behavior will then be the default.