Android Annotations build fails on Android Studio 0.5.1

Question

My build.gradle file has the following dependencies configuration:

dependencies {
    compile 'com.android.support:appcompat-v7:+'
    compile 'org.androidannotations:androidannotations:3.0.+'
    compile 'org.androidannotations:androidannotations-api:3.0.+'
    compile fileTree(dir: 'libs', include: ['*.jar'])
}

however the tag @EActivity is causing this error during the build:

Note: Resolve log file to 
    /home/ubuntu/MyApplication/app/build/classes/androidannotations.log
Note: Initialize AndroidAnnotations 3.0.1 with options {}
Note: Start processing for 1 annotations on 5 elements
error: Could not find the AndroidManifest.xml file, going up from path 
    [/home/ubuntu/MyApplication/app/build/classes/debug] found using dummy file []
    (max atempts: 
    file:///home/ubuntu/MyApplication/app/build/classes/debug/dummy1394454004584.java)
Note: Time measurements: [Whole Processing = 9 ms],
    [Extract Annotations = 6 ms], [Extract Manifest = 2 ms], 
Note: Finish processing
Note: Start processing for 0 annotations on 0 elements
Note: Time measurements: [Whole Processing = 1 ms], 
Note: Finish processing
warning: Unclosed files for the types '[dummy1394454004523, dummy1394454004584]';
    these types will not undergo annotation processing
1 error
1 warning
:app:compileDebugJava FAILED

I am using Android Studio 0.5.1, Gradle 1.11, and Gradle plugin 0.9.+.