Looks like they now run when I apply

kapt

on them, but the problem I had still persists :/

Kapt doesn’t run as part of compileJava, you have to specify APs explicitly using configuration

kapt

, actually I even not sure that compileJava runs Apt, I think Gradle now requires using configuration

annotationProcessor

for them

This is what I ended up with. The following sights may be disturbing.

protected void passArgument(KaptTask compileTask, String key, String value) {
		// Kapt doesn't provide an api to pass the AP args directly to the task so we need to do this hackery.
		CompilerPluginOptions options;
		if (compileTask instanceof KaptWithoutKotlincTask) {
			KaptWithoutKotlincTask task = (KaptWithoutKotlincTask) compileTask;
			// We are now entering the danger zone
			//noinspection KotlinInternalInJava aka @ts-ignore
			options = task.getProcessorOptions$kotlin_gradle_plugin();
		} else {
			KaptWithKotlincTask task = (KaptWithKotlincTask) compileTask;
			//noinspection KotlinInternalInJava aka @ts-ignore
			options = task.getPluginOptions$kotlin_gradle_plugin();
		}

		options.addPluginArgument(Kapt3KotlinGradleSubplugin.Companion.getKAPT_SUBPLUGIN_ID(), new SubpluginOption(key, value));
	}

Aaaand it doesn't work with

KaptWithKotlincTask

since it's encoded

actually I even not sure that compileJava runs Apt

Yes, it does, checked this. But it’s not recommended way and Gradle recommends to have annotation processors separately and use

annotationProcessor

annotation This behaviour probably can be changed with kapt.include.compile.classpath=true, but it’s not recommended