In tonights update I can report that the BitShares wallet API now supports covering of your short positions. While implementing this code I realized that the transaction verification for processing the covering of short positions will be a bit more complicated than I had originally thought. Next on my agenda is to get a robust algorithm for validating transactions that cover multiple short positions at once.
Things get much more complicated when a single transaction can have many different units, shorts, longs, etc and I have to have robust validation that prevents these combined inputs from being used to manipulate the margin requirements. Ultimately I may have to place some limits on the number and kinds of inputs a transaction can have. I will continue to post daily updates.