allowing/disallowing incremental mode from the Protege's GUI. Do not
reset the taxonomies when incremental mode is disallowed (a taxonomy can
still be queried). Placing the code which reads the config and sets the
reasoner's internal fields into the setConfigurationOptions method in
Reasoner (the factory calls this method after instantiation); it is also
called from Protege to change properties in an existing reasoner
instance.