scriptlibis missing from the User Extension list, so a more comprehensive list would be:
atom comp eyeonscript fu fuse setting toolbars prefs def scriptlib
I always loved how it keeps unsaved files open. Useful for having quick notes at hand that you'll be trashing later. Apparently they changed that default setting a while ago, but I'm so used to it being on, I would suggest having it on too. Settings -> Preferences -> Backup -> check “Remember current session for next launch” and “Enable session snapshot and periodic backup”.
When comparing files, the difference highlighted is unreadable. Maybe that could be fixed too, but I never tried doing that myself: