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The settings.js file is doing some preference storing in localstorage. This should be reconciled with the preferences service (which uses localStorage as a cache but also saves for user on server). I think the main missing piece is that Anton is using some notifications from localStorage to make sure that the editor updates on the fly. So we would need some kind of listener mechanism in the preferences service, probably based on what Anton did.
Resolved this. Using preferences local storage for now. There seem to be limitations with the user preferences. Will cut to that soon. Added some helper functions to preferences for settings. Will need to be reviewed/improved.
Submitted a fix for this.