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I have acidentally started FF as root, now when I start FF I have no bookmarks, no history, session save/restore does not work and the forward, back, refresh and stop buttons on the tool bar have greyed out and don't respond(tooltips stillappear though)
Is there something basic I've broken here, or will it need a clean FF instal?
Starting Firefox as root shouldn't permanently damage anything. All that happens generally is that it creates a new default profile in root's home directory (/root). Since root processes run under a different environment to other users, your regular user's profile should remain untouched.
Make sure that you've completely shut down the root instance of Firefox (you can use pkill firefox as root to kill all running processes if necessary). If the root instance somehow failed to shutdown completely then running the startup command will just bring up a new window of that instance. Once you're sure you've killed it completely, you can try starting it again as your regular user. If that doesn't bring it back with your regular profile, try running "firefox -ProfileManager" to select from available profiles. You can also check in ~/.mozilla/firefox to confirm the existence of your profiles.
It may have something to do with your themes being stored in your profile. Since the permissions are probably something like 0600, and have been changed to root, your user doesn't even have read rights....