any updates on this?

even without using JACK, we can do:

annotationProcessor "org.androidannotations:androidannotations:4.1.0"
compile "org.androidannotations:androidannotations-api:4.1.0"

instead of

apt "org.androidannotations:androidannotations:4.1.0"
compile "org.androidannotations:androidannotations-api:4.1.0"

but how do we pass the path of the manifest file to the new annotation processor?

apt {
    arguments {
        androidManifestFile variant.outputs[0]?.processResources?.manifestFile
        resourcePackageName android.defaultConfig.applicationId
    }
}

from http://tools.android.com/tech-docs/jackandjill we can do something like the following below:
but how do we handle all the different variants like the trick above (documented by https://bitbucket.org/hvisser/android-apt) ??

android {
...
    defaultConfig {
    ...
        javaCompileOptions { 
            annotationProcessorOptions {
                className 'com.example.MyProcessor'

        // Arguments are optional.
                arguments = [ foo : 'bar' ]
            }
        }
    }
    ...
}

[Question] How to configure androidannotations with Jack? #1853

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