Introduce Preferences object. This serves as the centralized repository of user
preferences.
At first, auto manipulator setting is stored in this.
Add a handler for Preferences. Also introduce json_object for easier JSON
parsing.
Update the client-local preferences (previously this relied on
RunningManipulators object updates. There is no longer an update for
preferences because the client should know what it sends back to the server).
Fix the wording about auto manipulators.