ProGuard Warning: Unable to write resource (write to duplicate zip)

First of all, I know this question already exists on stackoverflow, but I can't seem to solve it, although I've tried suggestions like not using -injar, using packagesOptions, etc.

I know the release will work, but I like clean builds. When I create signed apks. After cleaning the project, I get the following errors:

Warning:can't write resource [.readme] (Duplicate zip entry [classes.jar:.readme])
Warning:can't write resource [META-INF/LICENSE.txt] (Duplicate zip entry [joda-time-2.8.1.jar:META-INF/LICENSE.txt])
Warning:can't write resource [META-INF/NOTICE.txt] (Duplicate zip entry [joda-time-2.8.1.jar:META-INF/NOTICE.txt])

      

        
        
        
      

    

Sometimes commons-collections4-4.0.jar warnings appear instead of joda-time-2.8.1.jar (same .readme, license, notice).

I tried excluding those with packageOptions but that doesn't work.

Here is my build.gradle module

apply plugin: 'com.android.application'

android {
    compileSdkVersion 22
    buildToolsVersion "22.0.1"

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

    defaultConfig {
        applicationId 'com.example.myapp'
        minSdkVersion 15
        targetSdkVersion 22
        versionCode 1
        versionName '0.1'
    }

    buildTypes {
        release {
            minifyEnabled true
            proguardFiles getDefaultProguardFile('proguard-android-optimize.txt'), 'proguard-rules.pro'
        }
    }
}

dependencies {
    compile fileTree(include: ['*.jar'], dir: 'libs')
    compile 'com.android.support:appcompat-v7:22.2.1'
    compile 'org.apache.commons:commons-collections4:4.0'
    compile 'org.jsoup:jsoup:1.8.2'
    compile 'com.android.support:recyclerview-v7:22.2.0'
    compile 'com.android.support:cardview-v7:22.2.0'
    compile 'com.android.support:design:22.2.0'
    compile 'com.google.android.gms:play-services-gcm:7.5.0'
    compile 'joda-time:joda-time:2.8.1'
}

      

        
        
        
      

    

And my proguard-rules.pro file

# Defaults
-dontpreverify
-repackageclasses ''
-allowaccessmodification
-optimizations !code/simplification/arithmetic
-keepattributes *Annotation*

-keep public class * extends android.app.Activity
-keep public class * extends android.app.Application
-keep public class * extends android.app.Service
-keep public class * extends android.content.BroadcastReceiver
-keep public class * extends android.content.ContentProvider

-keep public class * extends android.view.View {
    public <init>(android.content.Context);
    public <init>(android.content.Context, android.util.AttributeSet);
    public <init>(android.content.Context, android.util.AttributeSet, int);
    public void set*(...);
}

-keepclasseswithmembers class * {
    public <init>(android.content.Context, android.util.AttributeSet);
}

-keepclasseswithmembers class * {
    public <init>(android.content.Context, android.util.AttributeSet, int);
}

-keepclassmembers class * implements android.os.Parcelable {
    static android.os.Parcelable$Creator CREATOR;
}

-keepclassmembers class **.R$* {
    public static <fields>;
}

-keep public class * extends android.support.v4.app.Fragment
-keep public class * extends android.app.Fragment

-keepnames class * implements java.io.Serializable

-keepclassmembers class * implements java.io.Serializable {
    static final long serialVersionUID;
    private static final java.io.ObjectStreamField[] serialPersistentFields;
    !static !transient <fields>;
    !private <fields>;
    !private <methods>;
    private void writeObject(java.io.ObjectOutputStream);
    private void readObject(java.io.ObjectInputStream);
    java.lang.Object writeReplace();
    java.lang.Object readResolve();
}

-keepclasseswithmembernames class * {
    native <methods>;
}
-keepclassmembers class * {
    public void *ButtonClicked(android.view.View);
}

# Use this to prevent errors in builds.
# usage of org.joda.time in this app does not need org.joda.convert
-dontwarn org.joda.convert.**


# Remove logs. Only when using 'proguard-android-optimize.txt'
-assumenosideeffects class android.util.Log {
    public static boolean isLoggable(java.lang.String, int);
    public static int v(...);
    public static int i(...);
    public static int w(...);
    public static int d(...);
    public static int e(...);
}

      

        
        
        
      

    

Thanks in advance.

EDIT: As per the request for a possible duplicate warning ( Proguard warnings "cannot write resource [META-INF / MANIFEST.MF] (Duplicate zip entry)" ). The user who asked the question said they are using multiple modules (instead of one) and are not hosting any files (due to sensitive data), so I don't know if this is the same case. Also tried all possible options from the first answer and none of them worked. The other answers didn't work (except for the -dontwarn option, which I won't use for obvious reasons).