Android Gradle plugin 0.7.0: "duplicate files during packaging of APK"

Question

Using Android Gradle plugin 0.7.0 with the following build.gradle:

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 ->
    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
        ]
    }
}

gives the error Duplicate files copied in APK META-INF/LICENSE.txt:

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: /U

Answer 1

As of Android Studio version 0.8.14

You should add:

 android {
     packagingOptions { 
         exclude 'META-INF/LICENSE.txt'
         exclude 'META-INF/NOTICE.txt'
         exclude '...'
     }
 }  

to your build.gradle file.

History:

According to comment 14 in this bug: https://issuetracker.google.com/issues/36982149#comment14 this is a bug in v0.7.0 of the Android Gradle plugin, and is due to be fixed soon in 0.7.1.

Here are the notes from that bug about the addition for 0.7.1:

0.7.1 is out with the fix for this.

The DSL to exclude files is:

android {
    packagingOptions {
        exclude 'META-INF/LICENSE.txt'
    }
}

You can add as many exclude statement as you want. The value is the archive path. No wildcard or glob support yet.

Filenames "LICENSE.txt" and "NOTICE.txt" are case sensitive. Please try out with "license.txt" and "notice.txt" as well.