The manual is being (slowly) updated. I try to do a little bit each time I am able to work on the software. It was indeed updated for 3.1 and 3.1.1, and it will be again for 3.2. But not entirely. Currently I'm working on chapter 18 (of 41), so not quite halfway done with the initial pass. After running through it once, I'll have to go back through the list of changes and make sure those changes are reflected in the manual (basically, anything I missed on the initial pass). I'm not sure exactly where I left off with 3.1.1 - probably somewhere around chapter 13.
Sorry for the delay! Truth is, most people don't read the user manual anyway, so it does get a slightly lower priority. If there are any specific chapters you want/need, you know I'll be happy to either update and post or just write up anything you need.