organize imports
ormat for oboparser
header update
added message to exception
replaced system.out with log
Changed variable rendering in Manchester OWL Syntax to preserve ns.

Variables like <urn:swrl#x> are rendered as ?x.
Strings like ?x are parsed as <urn:swrl#x>

Variables like <foo#x> are rendered as ?<foo#x>.
Strings like ?<foo#x> are parsed as <foo#x>.

This allows for parsing of simple forms and preserves namespaces in
roundtripping if a different namespace is used.
sync oboformat
updated serialVersionUID
javadoc fix
Warnings removed
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

Conflicts:
	api/src/main/java/org/semanticweb/owlapi/io/OWLParser.java
asPairwiseAxioms implemented for all nary axiom types