First of all, the Javadoc of ArrayList is somewhat wrong if we are talking about one-dimensional arrays, as it uses the method copyOf in Arrays. So clone() gives back a one-dimensional copy, at least since 1.5 (I didn't test further)! So that's what "shallow" means in Java: one-dimensional
You can read more here: http://www.javapractices.com/topic/TopicAction.do?Id=3. So clone() is no shallow copy! If you want a real shallow copy of a one-dimensional array, just reference it:
Array a = new Array();
Array b = a; //a is only a shallow copy, nice for synchronisation
Arrays in Java are tricky, also because Java does pass-by-value, but the values of arrays are only their pointers! In the other hand this allows us to synchronize the objects, which is a great thing. Still, there are some problems if you use arrays within arrays (or ArrayLists), because a clone() of the container array (or ArrayList) won't copy their values, only their references! So you simply shouldn't put any arrays into an array, you should only deal with objects in an array!
And Javadoc is difficult to understand sometimes, so give testing a try...
Have fun!