GPII-672: Raw Preferences server implemented and tests have been written for it
GPII-672: Removed the preferencesServer folder - this has now been replaced by the 'rawPreferencesServer' and the preferencesFramework
GPII-672: fixed some names in configuration and components, changing from user to the more correct rawPreferences
GPII-672: Added several functions to the ontologyHandler and cleaned up the code for it
GPII-672: Did some minor fixes in the ontology handler - loading the correct files, renaming, etc. Updated the preferencesFramework to now have a working REST GET handler and passing tests
GPII-672: added a gpii.ontologyHandler.addPrefsToRawPrefs function to the ontologyHandler that augments a raw preferences set with a given set of settings
GPII-672: preferencesFramework now supports GET, POST and PUT including tests