I just stumbled across an issue with the experimental plugin 0.3.1. I have three projects, two library projects and one app project. The app depends on both libraries and both libraries contain JNI code and depend on libgnustl_shared.so. Now the build fails in the packaging tasks with:
:app:dexDebug
:app:validateDebugSigning
:app:packageDebug FAILED
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':examples:dev_app:packageDebug'.
> Failed to add <path_to_app_folder>/build/intermediates/exploded-aar/app/lib_two/unspecified/jni/armeabi-v7a/libgnustl_shared.so
09:37:30.392 [DEBUG] [org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter] Executing actions for task ':examples:dev_app:packageDebug'.
09:37:30.392 [INFO] [org.gradle.api.internal.changedetection.changes.RebuildIncrementalTaskInputs] All input files are considered out-of-date for incremental task ':app:packageDebug'.
09:37:30.396 [DEBUG] [org.gradle.api.Project] Packaging dev_app-debug-unaligned.apk
09:37:30.396 [DEBUG] [org.gradle.api.Project] <path_to_project>/app/build/intermediates/res/resources-debug.ap_:
09:37:30.396 [DEBUG] [org.gradle.api.Project] => AndroidManifest.xml
...
09:37:31.384 [DEBUG] [org.gradle.api.Project] Native folder: <path_to_project>/app/build/intermediates/rs/debug/lib
09:37:31.384 [DEBUG] [org.gradle.api.Project] Native folder: <path_to_project>/app/build/intermediates/exploded-aar/lib_one/unspecified/jni
09:37:31.758 [DEBUG] [org.gradle.api.Project] => lib/armeabi-v7a/libgnustl_shared.so
09:37:31.866 [DEBUG] [org.gradle.api.Project] => lib/armeabi-v7a/libone.so
...
09:37:32.706 [DEBUG] [org.gradle.api.Project] Native folder: <path_to_project>/app/build/intermediates/exploded-aar/lib_two/unspecified/jni
09:37:32.706 [DEBUG] [org.gradle.api.Project] => lib/armeabi-v7a/libtwo.so
09:37:33.102 [DEBUG] [org.gradle.api.Project] => lib/armeabi-v7a/libgnustl_shared.so
09:37:33.121 [DEBUG] [org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter] Finished executing task ':examples:dev_app:packageDebug'