I was finally able to test 2.5 over the weekend and added a few tweaks to the code.
Here's what I hope is the final release.
As the new Manual gets formatted, you can view it at: http://code.google.com/p/ardupilot/wiki/ArduPilot25
Until the content is finally moved over the 2.4 manual is still a great resource.
Bonus - If you look check out the Waypoint_writer_25.pde file in the test suite, you can upload relative waypoints. This isn't supported in the config tool yet.
A lot of people were having trouble with the GPS code and LEDs. I reworked the GPS parsers today to iron out some things. They were nothing that would interfere with flight, but I highly recommend using this new version. I've also added the ability to scale down your plane's roll based on airspeed. This should help planes that turn faster when they go slower. We may tweak this a bit in the future, so I'm looking for feedback on it. Note you can always turn it off in your header file with this line:
#define AIRSPEED_TURN_P 1
see the header file for more instructions