Don't cache any literals in OWLDataFactoryInternalsImpl.

Every  call to any of the  getOWLLiteral method was building a brand new instance  anyway, even if there would have been a cache hit.

Overall improvement of about 9% when parsing Gene Ontology in FSS.  (mostly xsd:string literals)
Merge pull request #194 from sesuncedu/dont_cache_literals

Don't cache literals cos it's literally useless
Adding declarations when saving ontologies with profile violations #112

Do not add declarations for illegal punnings. 
Do not delete declarations.
Add declarations for functional format.

Big number of changes, mostly to do with tests (renamed a couple of
methods)
clean up a few minor warnings
An IRI with a space: hard parse error or %20 escape? #146

This commit assumes that %20 escape is fine
Files autogenerated by jjtree, which aren't used anywhere.
Merge pull request #196 from sesuncedu/remove_unused_jjtree_classes

Remove unused jjtree classes
OBO updated to 5.5 release
Fixes #198 A SubClassOf B will not parse
set to 4.0.0-SNAPSHOT
update to latest versions of depending libraries
updated readme
comment typos
IRI.getNCName(), IRI.prefixedBY() and IRI.getShortForm() added
removed warnings
IRI implements HasShortForm, getRemainder()
ensure manager and axioms collections do not used unguarded hashmaps
enumeration for atomic decomposition modes

In preparation for extra interfaces for reasoners