prefsCleaner?

[DerRockWolf]

I couldn't find any mention of the prefsCleaner.

How/When do you trigger the script?
It could be called via home.activation but maybe not a great idea because the Firefox profile shouldn't be in use when running prefsCleaner...

[dwarfmaster]

I do not use prefsCleaner. If an option is moved in arkenfox's user.js (for example if it is moved to 6050 or 9999), its name change so you will have an error when evaluating the configuration, and need to fix it manually.

Right now our approach work by parsing the user.js from arkenfox, and implementing everything on top of our parsed data, so we do not reuse any script from arkenfox.

[DerRockWolf]

From what I understood, the prefsCleaner is used to remove old (deprecated & removed) prefs from prefs.js.
prefs.js is generated by firefox on startup, and contains the prefs from user.js as well as all manually changed settings.
So with your solution you would additionally need to manually edit prefs.js.