If you want to add your classes (or any other resources) to your ShrinkWrap archive to a non-root location, you can use the following:

@Deployment
public static JavaArchive deploy() {

   // This is the classes and resources archive
   JavaArchive ar;
   ar = ShrinkWrap.create(JavaArchive.class, "resources.jar")
                  .addPackage(TestClass.class.getPackage());

   /*
    * The 'ar' archive will be added to the 'yourDir', so you'll
    * end with test.jar#/yourDir/TestClassPackage/TestClass.class
    */
   JavaArchive endArch;
   endArch = ShrinkWrap.create(JavaArchive.class, "test.jar")
                       .merge(ar, "yourDir");

   endArch.merge(ar, "yourDir");

   return endArch;
}