The documentation for the new gradle plugin is here: http://tools.android.com/tech-docs/new-build-system/user-guide

When I try to use AndroidAnnotations with it, I get the following error because AndroidManifest.xml is placed in build/manifests/debug, while AndroidAnnotations looks up from build/classes/debug.

error: Unexpected error. Please report an issue on AndroidAnnotations, with the following content: java.lang.IllegalStateException: Could not find the AndroidManifest.xml file, going up from path [/Users/devesh/Google Drive/eclipseworkspace/dropsentry/SensorClient/build/classes/debug] found using dummy file [file:///Users/devesh/Google%20Drive/eclipseworkspace/dropsentry/SensorClient/build/classes/debug/dummy1362074314049.java](max atempts: 10)
at com.googlecode.androidannotations.helper.AndroidManifestFinder.findManifestInParentsDirectories(AndroidManifestFinder.java:156)
at com.googlecode.androidannotations.helper.AndroidManifestFinder.findManifestFileThrowing(AndroidManifestFinder.java:93)
at com.googlecode.androidannotations.helper.AndroidManifestFinder.extractAndroidManifestThrowing(AndroidManifestFinder.java:65)
at com.googlecode.androidannotations.helper.AndroidManifestFinder.extractAndroidManifest(AndroidManifestFinder.java:55)
at com.googlecode.androidannotations.AndroidAnnotationProcessor.extractAndroidManifest(AndroidAnnotationProcessor.java:388)
at com.googlecode.androidannotations.AndroidAnnotationProcessor.processThrowing(AndroidAnnotationProcessor.java:358)
at com.googlecode.androidannotations.AndroidAnnotationProcessor.process(AndroidAnnotationProcessor.java:341)
at com.sun.tools.javac.processing.JavacProcessingEnvironment.callProcessor(JavacProcessingEnvironment.java:627)
at com.sun.tools.javac.processing.JavacProcessingEnvironment.discoverAndRunProcs(JavacProcessingEnvironment.java:556)
at com.sun.tools.javac.processing.JavacProcessingEnvironment.doProcessing(JavacProcessingEnvironment.java:701)

I'll file a separate documentation bug to update the documentation to include the new Android Gradle plugin.