A working solution has been submitted on the github issue: source folders have to be configured via gradle. So the configuration for android part should look like this :
android {
compileSdkVersion 18
buildToolsVersion "18.0.1"
defaultConfig {
minSdkVersion 7
targetSdkVersion 18
}
sourceSets {
main {
manifest.srcFile 'src/main/AndroidManifest.xml'
java.srcDirs = ['src/main/java', 'YOUR_OTHER_PRODUCTION_SOURCE_FOLDER']
resources.srcDirs = ['src/main/res']
res.srcDirs = ['src/main/res']
}
}
}
Also, I agree with Eugen, you really should use the new android-apt plugin. This has been explained on the wiki page of AA project. I'm gonna add a part of how to configure AA on Android studio to clarify this point.