Estoy usando Android Studio 2.0 en Windows 7. Al compilar mi proyecto de Android, aparece el siguiente error:

:app:transformResourcesWithMergeJavaResForDebug FAILED

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':app:transformResourcesWithMergeJavaResForDebug'.
> com.android.build.api.transform.TransformException: com.android.builder.packaging.DuplicateFileException: Duplicate files copied in APK com/google/appengine/repackaged/org/apache/commons/codec/language/bm/sep_approx_spanish.txt
File1: C:\Users\USER\.gradle\caches\modules-2\files-2.1\com.google.appengine\appengine-api-1.0-sdk\1.9.28\e92c18272b555027d9ec666e7a89162f10638314\appengine-api-1.0-sdk-1.9.28.jar
File2: C:\Users\USER\.gradle\caches\modules-2\files-2.1\com.google.appengine\appengine-endpoints\1.9.28\bf2e8a74bd28e388b3487fc78a0c7adfa592fd5d\appengine-endpoints-1.9.28.jar`

He estado cavando durante horas y no puedo ver nada que cause esto. He eliminado .gradle en mi directorio de inicio, pero simplemente lo reconstruye de todos modos. ¿Sabe alguien qué causa ésto?

Salida completa de gradle:

Executing tasks: [:app:clean, :app:generateDebugSources, :app:mockableAndroidJar, :app:prepareDebugUnitTestDependencies, :app:generateDebugAndroidTestSources, :app:assembleDebug]

Configuration on demand is an incubating feature.
WARNING: Dependency org.apache.httpcomponents:httpclient:4.0.1 is ignored for debug as it may be conflicting with the internal version provided by Android.
     In case of problem, please repackage it with jarjar to change the class packages
WARNING: Dependency org.apache.httpcomponents:httpclient:4.0.1 is ignored for release as it may be conflicting with the internal version provided by Android.
     In case of problem, please repackage it with jarjar to change the class packages
Incremental java compilation is an incubating feature.
:app:clean
:app:preBuild UP-TO-DATE
:app:preDebugBuild UP-TO-DATE
:app:checkDebugManifest
:app:preReleaseBuild UP-TO-DATE
:backend:appengineDownloadSdk
:backend:compileJava
:backend:processResources UP-TO-DATE
:backend:classes
:backend:appengineEndpointsGetClientLibs UP-TO-DATE
:backend:appengineEndpointsExpandClientLibs UP-TO-DATE
:backend:compileEndpointsSrcJava
:backend:processEndpointsSrcResources UP-TO-DATE
:backend:endpointsSrcClasses
:backend:_appengineEndpointsAndroidArtifact UP-TO-DATE
:backend:jar UP-TO-DATE
:app:prepareComAndroidSupportAnimatedVectorDrawable2330Library
:app:prepareComAndroidSupportAppcompatV72330Library
:app:prepareComAndroidSupportSupportV42330Library
:app:prepareComAndroidSupportSupportVectorDrawable2330Library
:app:prepareComGoogleAndroidGmsPlayServicesAuth840Library
:app:prepareComGoogleAndroidGmsPlayServicesBase840Library
:app:prepareComGoogleAndroidGmsPlayServicesBasement840Library
:app:prepareComGoogleAndroidGmsPlayServicesMeasurement840Library
:app:prepareDebugDependencies
:app:compileDebugAidl
:app:compileDebugRenderscript
:app:generateDebugBuildConfig
:app:generateDebugAssets UP-TO-DATE
:app:mergeDebugAssets
:app:generateDebugResValues UP-TO-DATE
:app:processDebugGoogleServices
:app:generateDebugResources
:app:mergeDebugResources
:app:processDebugManifest
:app:processDebugResources
:app:generateDebugSources
:app:mockableAndroidJar UP-TO-DATE
:app:preDebugUnitTestBuild UP-TO-DATE
:app:prepareDebugUnitTestDependencies
:app:preDebugAndroidTestBuild UP-TO-DATE
:app:prepareDebugAndroidTestDependencies
:app:compileDebugAndroidTestAidl
:app:processDebugAndroidTestManifest
:app:compileDebugAndroidTestRenderscript
:app:generateDebugAndroidTestBuildConfig
:app:generateDebugAndroidTestAssets UP-TO-DATE
:app:mergeDebugAndroidTestAssets
:app:generateDebugAndroidTestResValues UP-TO-DATE
:app:generateDebugAndroidTestResources
:app:mergeDebugAndroidTestResources
:app:processDebugAndroidTestResources
:app:generateDebugAndroidTestSources
:app:compileDebugJavaWithJavac
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.

:app:compileDebugNdk UP-TO-DATE
:app:compileDebugSources
:app:buildInfoDebugLoader
:app:transformClassesWithExtractJarsForDebug
:app:transformClassesWithInstantRunVerifierForDebug
:app:transformClassesWithJavaResourcesVerifierForDebug UP-TO-DATE
:app:mergeDebugJniLibFolders
:app:transformNative_libsWithMergeJniLibsForDebug
:app:processDebugJavaRes UP-TO-DATE
:app:transformResourcesWithMergeJavaResForDebug FAILED

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':app:transformResourcesWithMergeJavaResForDebug'.
> com.android.build.api.transform.TransformException:     com.android.builder.packaging.DuplicateFileException: Duplicate files copied in APK com/google/appengine/repackaged/org/apache/commons/codec/language/bm/sep_approx_spanish.txt
File1: C:\Users\USER\.gradle\caches\modules-2\files-2.1\com.google.appengine\appengine-api-1.0-sdk\1.9.28\e92c18272b555027d9ec666e7a89162f10638314\appengine-api-1.0-sdk-1.9.28.jar
File2: C:\Users\USER\.gradle\caches\modules-2\files-2.1\com.google.appengine\appengine-endpoints\1.9.28\bf2e8a74bd28e388b3487fc78a0c7adfa592fd5d\appengine-endpoints-1.9.28.jar


* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 15.364 secs

Por lo que puedo decir, es un conflicto entre dos dependencias:

dependencies {
  appengineSdk 'com.google.appengine:appengine-java-sdk:1.9.28'
  compile 'com.google.appengine:appengine-endpoints:1.9.28'
  compile 'com.google.appengine:appengine-endpoints-deps:1.9.28'
  compile 'javax.servlet:servlet-api:2.5'
  compile 'com.google.http-client:google-http-client-jackson2:1.20.0'
  compile 'com.google.http-client:google-http-client-gson:1.19.0'
}

Creo que son estas dos dependencias:

appengineSdk 'com.google.appengine:appengine-java-sdk:1.9.28'
compile 'com.google.appengine:appengine-endpoints:1.9.28'
compile 'com.google.appengine:appengine-endpoints-deps:1.9.28'

No puedo eliminar ninguno de estos, ya que causa errores de compilación en el módulo back-end. Sin embargo, parece que esas dos dependencias son casi idénticas. ¿Deberían estar ambos allí? Cualquier consejo es apreciado!