Same output path lead to java.lang.ClassNotFoundException

[ashqal]

Copying classes to /Users/Asha/AndroidStudioProjects/AndroidGradleTransformTest/app/build/intermediates/transforms/MyTransform_1/debug/jars/1/10/classes.jar
Copying classes to /Users/Asha/AndroidStudioProjects/AndroidGradleTransformTest/app/build/intermediates/transforms/MyTransform_1/debug/jars/1/10/classes.jar
Copying classes to /Users/Asha/AndroidStudioProjects/AndroidGradleTransformTest/app/build/intermediates/transforms/MyTransform_1/debug/jars/1/10/classes.jar
Copying classes to /Users/Asha/AndroidStudioProjects/AndroidGradleTransformTest/app/build/intermediates/transforms/MyTransform_1/debug/jars/1/10/classes.jar

as you see, the classes.jar was override three times, so some classes are missing.
I think you may fix it like this

for (TransformInput input: inputs)
{
    int i = 0;
    for (JarInput jarInput: input.jarInputs) {
        i++;
        File dest = outputProvider.getContentLocation("classes" + i, jarInput.contentTypes, jarInput.scopes, Format.JAR)
        println("Copying jarInput " + jarInput.name + " to " + dest.absolutePath)
        FileUtils.copyFile(jarInput.getFile(), dest)
    }
}