I wanted to post to this forum because it's in Google's index for the Tremulous error message couldn't write to autogen.cfg
Got this message after installing Tremulous from the Ubuntu Repositories and even after downloading a .deb file and installing that way.
By running the game as root, the autogen.cfg file was able to create itself.
In Ubuntu you can run nautilus as root by doing an ALT+F2 then type
gksudo nautilus
Enter your admin password and then if you have a 'short cut' to your Tremulous game on the desk top navigate to your home directory on the root of the File System then your home folder and then your desktop folder - Click Tremulous from there and run it.
Once your in and you change your nickname in the game or any settings and then apply it in the Options > System section it will now write the autogen.cfg without a problem.
Now if you run it once like this you can run it the next time the normal way, you don't have to go through these steps again.
This was the only error I was seeing on my install of Tremulous from the Ubuntu Repositorys (Go into Synaptic and search for 'Tremuous' to install), so this may not cure your problem if you see more errors or you can't even run the game.
I like Windows so this was easiest way for me. I'm sure a Linux Guru is going to laugh at this but I'm new to Linux and found this to be pretty easy. And above all else it worked.
Happy Hunting.
