Both Jacob and Rusty have been working on ArduSub code here.
The version I have running is a hacked version of the ArduCopter-3.2.1 branch. That can be found at https://github.com/jaxxzer/ardupilot-rov.git
I will not be making any pull requests, because I just hacked apart the hexacopter code for proof of concept. TCIII, is correct. Rusty and I are working on the master branch and going about it proper, so it will hopefully be pulled in.
Fantastic. I did not realize you were working with Rusty. I will talk to him about it and make sure it gets pulled in