Unfortunately we have no solution for the time being.
In the meantime we estimated a possibility to port Fribidi library to Java, which should be able to work with extended arabic. However the first working prototype just worked wrongly with our tests.
It seems the only possible solution is to patch our current ligaturizer, as a porting of Fribidi appears as a new bunch of problems. If you’d like to contribute, please contact support pd4ml com. We’ll send you the classes and some our comments what needs to be done. It looks like a table with isolated, final, initial and medial glyph shape references needs to be extended with new chars. Without a knowledge of Arabic scripting it does not seem to be an easy task.