fixes 2764: settings defined in seetings.yaml file are now read-only

I'm not entirely sure what to do about the current behaviour for settings defined in the configuration file -- they are used to set default values. 
 - Should this behaviour be preserved? I think it's awkward.
 - If we want to use the configuration file to set default values, should those be updated when configuration file changes? I think so, as this would be less confusing than current semantic (default value can only be set once).