I have finally been able to get back to playing some Aurora today, although I still haven't gone through all the outstanding posts. However I have added a couple of new functions for v3.2. You can now transfer ships from one empire to another using a small section on the Miscellaneous tab of the ship window. You select the ship, select the alien empire (which must be one you know about) and press Transfer. You have the option to transfer a commander along with his ship. This is similar to selling a ship on the market window so a new fleet and a new class (if required) are created for the alien empire.
A similar function has been added to the Additional Information tab of the Fleet window, except you transfer the whole fleet instead of just one ship. These new functions will be useful for transfering forces to an ally rather then selling them or in a role-play type situation where a ship may surrender to an enemy. At some point I guess I should add some rules for ships automatically surrendering in the same way as populations.
Steve