title: Duplicate Zip Entry after Gradle Plugin v0.13.1
body: <p>I've been using the Gradle Android plugin v0.12 but I decided to upgrade to the new version, because I needed the new functionality (and the improved speed is always a plus).</p>
  
  <p>After updating to the new v0.13.1, I keep getting the "Duplicate Zip Entry" (from Proguard) while everything worked before. The full error:</p>
  
  <blockquote>
    <p>java.io.IOException: Can't write [/Users/.../classes-proguard/netherlands/release/classes.jar] (Can't read [/Users/.../.gradle/caches/modules-2/files-2.1/org.apache.commons/commons-io/1.3.2/b6dde38349ba9bb5e6ea6320531eae969985dae5/commons-io-1.3.2.jar(;;;;;;!META-INF/MANIFEST.MF)] (Duplicate zip entry [commons-io-1.3.2.jar:org/apache/commons/io/CopyUtils.class])) (CopyUtils was FileUtils before).</p>
  </blockquote>
  
  <p>I'm using following packaging options: packagingOptions </p>
  
  <pre><code>{ 
     exclude 'AndroidManifest.xml' 
     exclude 'META-INF/DEPENDENCIES' 
     exclude 'META-INF/notice.txt' 
     exclude 'META-INF/license.txt' 
     exclude 'META-INF/LICENSE.txt' 
     exclude 'META-INF/NOTICE.txt' 
     exclude 'META-INF/MANIFEST.MF' 
     exclude '!META-INF/MANIFEST.MF' 
     exclude 'META-INF/services/javax.annotation.processing.Processor' 
  }
  </code></pre>
  
  <p>As you can tell, I'm excluding the manifest files...</p>
  
  <p>Just to test it, I changed back to version 0.12.0 and everything works again, back to 0.13.* and it breaks (but I need 0.13.*)!</p>
  
  <p>Further, I'm using the following libraries: </p>
  
  <ol>
  <li>Robospice </li>
  <li>Retrofit</li>
  <li>OkHttp</li>
  <li>Dart</li>
  <li>Icepick</li>
  <li>Butterknife</li>
  <li>Crouton</li>
  <li>SmoothProgressBar</li>
  <li>NineoldsAndroid (in library of BetterPickers)</li>
  </ol>
  
  <p>Did anyone encounter this issue too? If so, can anyone please help me out (been breaking my head for 2 days on this issue now!)? Thanks!</p>