Include contract main classes
Updated the OWLParser documentation to reflect the fact that parsers
*add* the axioms of the parsed ontology to an existing ontology
object, rather than making the ontology object contain *exactly* the
axioms of the parsed ontology.  Also cleaned up the links to
OWLManager#makeLoadImportRequest.

Added notes that the typical useage of OWLParsers is by
OWLOntologyManagers to populate empty ontology objects, and clarified
ambiguous wording about the documentIRI argument (don't conflate an
IRI that an ontology can be loaded from and the ontology IRI of the
ontology).

Contributed by Joshua Taylor, with suggestions from Peter Ansell and
minor changes by Ignazio