enumeration for atomic decomposition modes

In preparation for extra interfaces for reasoners
Fix #207 OBO parser fails when a comment is in the date tag

Also add workaround for OBO parser does not handle the [Instance] stanza
#208
Fix #215 getOntology(OWLOntologyID) can throw a NPE
update AD related interface as suggested by Dmitry
Fix #217 Manchester abstract renderer in 3.5+ swallows exceptions but
prints stacktrace
bug fix: incomplete OBO writes

Always flush the buffer after writing
bug fix: missing [] for synonyms
add test for missing synonym brackets
bug fix: missing labels in comments

Use the whole ontology, and not only the OBO doc, to resolve names
more misbehaving comparators. Wrapped the sorting in a method to reuse
it
fix bug
eclise settings committed
Clearer error message from OBO when invalid IRIs are created.
Fix #251 OBO parser for 1.4 cannot handle some 1.2 ontologies

Reintroduced OBO parser for 1.2 from OWLAPITOOLS for backwards
compatibility
fixed java 6 compatibility
fix #253 StructuralReasoner.getSameIndividuals does not behave as
advertised
corrected java 7 infiltrations
fix #254 OWLAsymmetricObjectPropertyAxiom not rendered in DL Syntax
improved performance of OWLAxiomImpl.equals
Test for #274 Turtle parser problem when parsing scientific notation