JSON preferences (still using prefs panel)

Switches storage of preferences to JSON stored file, but retains the use of the preferences panel to set them.  Migrates all stored preferences to use JSON stored file.

@devoncarew 
Lets remove the code to migrate old preferences - this will be a very rare event, and user's don't have many prefs currently. We'll also be able to remove the _migrateFromStore method and the firstRun getter.