title: Android Gradle plugin 0.7.0: "duplicate files during packaging of APK"
body: <p>Using Android Gradle plugin 0.7.0 with the following <code>build.gradle</code>:</p>
  
  <pre><code>buildscript {
      repositories {
          mavenCentral()
      }
  
      dependencies {
          classpath 'com.android.tools.build:gradle:0.7.0'
      }
  }
  
  apply plugin: 'android'
  
  repositories {
      maven { url "https://android-rome-feed-reader.googlecode.com/svn/maven2/releases" }
      maven { url "http://dl.bintray.com/populov/maven" }
      mavenCentral()
  }
  
  android {
      compileSdkVersion 19
      buildToolsVersion '18.1.1'
  
      defaultConfig {
          minSdkVersion 9
          targetSdkVersion 19
      }
      buildTypes {
          release {
              runProguard true
              proguardFile getDefaultProguardFile('proguard-android-optimize.txt')
          }
      }
      productFlavors {
          defaultFlavor {
              proguardFile 'proguard-rules.txt'
          }
      }
      sourceSets {
          instrumentTest.setRoot('src/instrumentTest')
      }
  }
  
  configurations {
      apt
  }
  
  ext.androidAnnotationsVersion = '2.7.1';
  
  dependencies {
      compile 'com.android.support:support-v4:18.0.0'
  
      compile 'com.viewpagerindicator:library:2.4.1@aar'
  
      compile 'com.google.code.android-rome-feed-reader:android-rome-feed-reader:1.0.0-r2'
      compile 'org.jdom:jdom:1.1.1-android-fork'
  
      apt "com.googlecode.androidannotations:androidannotations:${androidAnnotationsVersion}"
      compile "com.googlecode.androidannotations:androidannotations-api:${androidAnnotationsVersion}"
  
      compile 'com.google.code.gson:gson:2.2.4'
      compile 'com.j256.ormlite:ormlite-android:4.47'
      compile 'com.j256.ormlite:ormlite-core:4.47'
      compile 'org.springframework.android:spring-android-core:1.0.1.RELEASE'
      compile 'org.springframework.android:spring-android-rest-template:1.0.1.RELEASE'
      compile 'com.prolificinteractive:actionbarsherlock:4.3.1@aar'
  
      compile 'com.google.code.geocoder-java:geocoder-java:0.15'
  
      compile files('libs/CWAC-Pager.jar')
  }
  
  android.applicationVariants.all { variant -&gt;
      aptOutput = file("${project.buildDir}/source/apt_generated/${variant.dirName}")
      println "****************************"
      println "variant: ${variant.name}"
      println "manifest:  ${variant.processResources.manifestFile}"
      println "aptOutput:  ${aptOutput}"
      println "****************************"
  
      variant.javaCompile.doFirst {
          println "*** compile doFirst ${variant.name}"
          aptOutput.mkdirs()
          variant.javaCompile.options.compilerArgs += [
                  '-processorpath', configurations.apt.getAsPath(),
                  '-AandroidManifestFile=' + variant.processResources.manifestFile,
                  '-s', aptOutput
          ]
      }
  }
  </code></pre>
  
  <p>gives the error <code>Duplicate files copied in APK META-INF/LICENSE.txt</code>:</p>
  
  <pre><code>WARNING: Dependency commons-logging:commons-logging:1.0.4 is ignored for defaultFlavorDebug 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 commons-logging:commons-logging:1.0.4 is ignored for defaultFlavorRelease 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
  Creating properties on demand (a.k.a. dynamic properties) has been deprecated and is scheduled to be removed in Gradle 2.0. Please read http://gradle.org/docs/current/dsl/org.gradle.api.plugins.ExtraPropertiesExtension.html for information on the replacement for dynamic properties.
  Deprecated dynamic property: "aptOutput" on "com.android.build.gradle.internal.api.ApplicationVariantImpl_Decorated@5705013c", value: "/Users/david/Developer...".
  ****************************
  variant: defaultFlavorDebug
  manifest:  /Users/david/Developer/.../build/manifests/defaultFlavor/debug/AndroidManifest.xml
  aptOutput:  /Users/david/Developer/.../build/source/apt_generated/defaultFlavor/debug
  ****************************
  Deprecated dynamic property "aptOutput" created in multiple locations.
  ****************************
  variant: defaultFlavorRelease
  manifest:  /Users/david/Developer/.../build/manifests/defaultFlavor/release/AndroidManifest.xml
  aptOutput:  /Users/david/Developer/.../build/source/apt_generated/defaultFlavor/release
  ****************************
  :TravelGuard:compileDefaultFlavorDebugNdk UP-TO-DATE
  :TravelGuard:preBuild UP-TO-DATE
  :TravelGuard:preDefaultFlavorDebugBuild UP-TO-DATE
  :TravelGuard:preDefaultFlavorReleaseBuild UP-TO-DATE
  :TravelGuard:prepareComProlificinteractiveActionbarsherlock431Library UP-TO-DATE
  :TravelGuard:prepareComViewpagerindicatorLibrary241Library UP-TO-DATE
  :TravelGuard:prepareDefaultFlavorDebugDependencies
  :TravelGuard:compileDefaultFlavorDebugAidl UP-TO-DATE
  :TravelGuard:compileDefaultFlavorDebugRenderscript UP-TO-DATE
  :TravelGuard:generateDefaultFlavorDebugBuildConfig UP-TO-DATE
  :TravelGuard:mergeDefaultFlavorDebugAssets UP-TO-DATE
  :TravelGuard:mergeDefaultFlavorDebugResources UP-TO-DATE
  :TravelGuard:processDefaultFlavorDebugManifest UP-TO-DATE
  :TravelGuard:processDefaultFlavorDebugResources UP-TO-DATE
  :TravelGuard:generateDefaultFlavorDebugSources UP-TO-DATE
  :TravelGuard:compileDefaultFlavorDebugJava
  *** compile doFirst defaultFlavorDebug
  /Users/david/Developer/.../src/main/java/com/travelguard/service/TravelGuardService.java:53: cannot find symbol
  symbol  : class TravelGuardPrefs_
  location: class com.travelguard.service.TravelGuardService
      TravelGuardPrefs_ travelGuardPrefs;
      ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/CategoriesActivity.java:14: cannot find symbol
  symbol  : class AssistanceFragment_
  location: package com.travelguard.ui.fragments
  import com.travelguard.ui.fragments.AssistanceFragment_;
                                     ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/CategoriesActivity.java:16: cannot find symbol
  symbol  : class CategoryFragment_
  location: package com.travelguard.ui.fragments
  import com.travelguard.ui.fragments.CategoryFragment_;
                                     ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/CategoriesActivity.java:17: cannot find symbol
  symbol  : class ContactFragment_
  location: package com.travelguard.ui.fragments
  import com.travelguard.ui.fragments.ContactFragment_;
                                     ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/CountriesActivity.java:25: cannot find symbol
  symbol  : class TravelGuardPrefs_
  location: package com.travelguard.service
  import com.travelguard.service.TravelGuardPrefs_;
                                ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/CountriesActivity.java:44: cannot find symbol
  symbol  : class TravelGuardPrefs_
  location: class com.travelguard.ui.CountriesActivity
      TravelGuardPrefs_ travelGuardPrefs;
      ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/InstructionsActivity.java:18: cannot find symbol
  symbol  : class AssistanceFragment_
  location: package com.travelguard.ui.fragments
  import com.travelguard.ui.fragments.AssistanceFragment_;
                                     ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/InstructionsActivity.java:19: cannot find symbol
  symbol  : class ContactFragment_
  location: package com.travelguard.ui.fragments
  import com.travelguard.ui.fragments.ContactFragment_;
                                     ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/InstructionsActivity.java:21: cannot find symbol
  symbol  : class InstructionsFragment_
  location: package com.travelguard.ui.fragments
  import com.travelguard.ui.fragments.InstructionsFragment_;
                                     ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/MainActivity.java:36: cannot find symbol
  symbol  : class TravelGuardPrefs_
  location: package com.travelguard.service
  import com.travelguard.service.TravelGuardPrefs_;
                                ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/MainActivity.java:40: cannot find symbol
  symbol  : class AssistanceFragment_
  location: package com.travelguard.ui.fragments
  import com.travelguard.ui.fragments.AssistanceFragment_;
                                     ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/MainActivity.java:41: cannot find symbol
  symbol  : class ContactFragment_
  location: package com.travelguard.ui.fragments
  import com.travelguard.ui.fragments.ContactFragment_;
                                     ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/MainActivity.java:55: cannot find symbol
  symbol  : class TravelGuardPrefs_
  location: class com.travelguard.ui.MainActivity
      TravelGuardPrefs_ travelGuardPrefs;
      ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/TermsActivity.java:17: cannot find symbol
  symbol  : class TravelGuardPrefs_
  location: package com.travelguard.service
  import com.travelguard.service.TravelGuardPrefs_;
                                ^
  /Users/david/Developer/.../src/main/java/com/travelguard/ui/TermsActivity.java:23: cannot find symbol
  symbol  : class TravelGuardPrefs_
  location: class com.travelguard.ui.TermsActivity
      TravelGuardPrefs_ travelGuardPrefs;
      ^
  Note: Starting AndroidAnnotations annotation processing
  Note: AndroidManifest.xml file found: /Users/david/Developer/.../build/manifests/defaultFlavor/debug/AndroidManifest.xml
  Note: Number of files generated by AndroidAnnotations: 22
  Note: Generating source file: com.travelguard.service.SmartTravellerService_
  Note: Generating source file: com.travelguard.service.SmartTravellerWebservice_
  Note: Generating source file: com.travelguard.service.TravelGuardPrefs_
  Note: Generating source file: com.travelguard.service.TravelGuardService_
  Note: Generating source file: com.travelguard.service.TravelGuardWebservice_
  Note: Generating source file: com.travelguard.ui.AdviceActivity_
  Note: Generating source file: com.travelguard.ui.CategoriesActivity_
  Note: Generating source file: com.travelguard.ui.ContactDetailActivity_
  Note: Generating source file: com.travelguard.ui.ContactListActivity_
  Note: Generating source file: com.travelguard.ui.ContactTravelGuardActivity_
  Note: Generating source file: com.travelguard.ui.CountriesActivity_
  Note: Generating source file: com.travelguard.ui.InformationActivity_
  Note: Generating source file: com.travelguard.ui.InstructionsActivity_
  Note: Generating source file: com.travelguard.ui.MainActivity_
  Note: Generating source file: com.travelguard.ui.TermsActivity_
  Note: Generating source file: com.travelguard.ui.TravelGuardActivity_
  Note: Generating source file: com.travelguard.ui.fragments.AdviceDetailFragment_
  Note: Generating source file: com.travelguard.ui.fragments.AdviceFragment_
  Note: Generating source file: com.travelguard.ui.fragments.AssistanceFragment_
  Note: Generating source file: com.travelguard.ui.fragments.CategoryFragment_
  Note: Generating source file: com.travelguard.ui.fragments.ContactFragment_
  Note: Generating source file: com.travelguard.ui.fragments.InstructionsFragment_
  Note: Time measurements: [Whole Processing = 913 ms], [Generate Sources = 358 ms], [Extract Manifest = 163 ms], [Process Annotations = 158 ms], [Extract Annotations = 120 ms], [Validate Annotations = 82 ms], [Find R Classes = 28 ms],
  Note: Time measurements: [Whole Processing = 0 ms],
  Note: Time measurements: [Whole Processing = 0 ms],
  warning: The following options were not recognized by any processor: '[androidManifestFile]'
  Note: /Users/david/Developer/.../src/main/java/com/travelguard/ui/ContactDetailActivity.java uses or overrides a deprecated API.
  Note: Recompile with -Xlint:deprecation for details.
  Note: /Users/david/Developer/.../src/main/java/com/travelguard/service/SmartTravellerService.java uses unchecked or unsafe operations.
  Note: Recompile with -Xlint:unchecked for details.
  :TravelGuard:preDexDefaultFlavorDebug UP-TO-DATE
  :TravelGuard:dexDefaultFlavorDebug
  :TravelGuard:processDefaultFlavorDebugJavaRes UP-TO-DATE
  :TravelGuard:validateDebugSigning
  :TravelGuard:packageDefaultFlavorDebug
  Error: duplicate files during packaging of APK /Users/david/Developer/.../build/apk/TravelGuard-defaultFlavor-debug-unaligned.apk
      Path in archive: META-INF/LICENSE.txt
      Origin 1: /Users/david/.gradle/caches/modules-2/files-2.1/commons-httpclient/commons-httpclient/3.1/964cd74171f427720480efdec40a7c7f6e58426a/commons-httpclient-3.1.jar
      Origin 2: /Users/david/.gradle/caches/modules-2/files-2.1/commons-codec/commons-codec/1.2/397f4731a9f9b6eb1907e224911c77ea3aa27a8b/commons-codec-1.2.jar
  :TravelGuard:packageDefaultFlavorDebug FAILED
  
  FAILURE: Build failed with an exception.
  
  * What went wrong:
  Execution failed for task ':TravelGuard:packageDefaultFlavorDebug'.
  &gt; Duplicate files copied in APK META-INF/LICENSE.txt
      File 1: /Users/david/.gradle/caches/modules-2/files-2.1/commons-httpclient/commons-httpclient/3.1/964cd74171f427720480efdec40a7c7f6e58426a/commons-httpclient-3.1.jar
      File 2: /Users/david/.gradle/caches/modules-2/files-2.1/commons-httpclient/commons-httpclient/3.1/964cd74171f427720480efdec40a7c7f6e58426a/commons-httpclient-3.1.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: 21.957 secs
  </code></pre>
  
  <p>Things were working fine this morning before I updated Android Studio. Any ideas?</p>
  
  <p>EDIT: I was able to temporarily fix it by running commands like</p>
  
  <pre><code>zip -d spring-android-core-1.0.1.RELEASE.jar META-INF/notice.txt
  </code></pre>
  
  <p>until all the duplicate errors went away.</p>