Deploying Firefox 18 in a library. PCs are Linux (Ubuntu 12.04). I have a configured user.js to install on each PC that works great. But I note in testing that if a user on one of these PCs goes into Troubleshooting and clicks Reset, it eradicates the directory which contains user.js -- this is not so great.
So this new tool forces me to use mozilla.cfg on each machine?
Yes, the only way to prevent prefs from not getting initialized like a user.js file does is with a mozilla.cfg file.
The mozilla.cfg file is in the installation folder and you would need root access to modify files in this location, so if it is important that prefs are initialized on every start then you need to use such a file.
You also only need one such file for all profiles from all users, so it is much easier to maintain if changes are needed.
You can use these functions in mozilla.cfg:
defaultPref(); // set new default value
pref(); // set pref, but allow changes in current session
lockPref(); // lock pref, disallow changes