refactored OWLAxiomIndex, refactored Internals, added getAxioms()

OWLOntology now exposes a new method for searching for axioms referring
an entity, abstracting all various getAxiomsBy... methods.
Includes #97 Fixes to TutorialSnippets Test:

 Load Pizza Ontology from local file using an Auto IRI Mapper set via
finding Resource via ClassLoader.

 Avoid writing to console by creating simple
LoggingReasonerProgressMonitor (which might be a sensible class
 outside the test framework).

 Add a few not-null assertions in otherwise empty loops.

 In testMergedOntology, create an example, non-empty ontology to allow
so that merge runs and existing axioms pass.
Dire indeed!
added a fixed rdfxml test file to remove apparent errors.
     <owl:Class rdf:resource="Dead"/>
   replaced with
       <owl:allValuesFrom rdf:resource="Dead"/>.

     <rdfs:range
rdfs:Datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger"/>
   replaced with
     <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#nonNegativeInteger"/>

  Axiom count in RIoTest reduced from 93 to 92.
more refactoring of OWLAxiomIndex

Note: switching MapPointer from lazy to eager insertion makes some unit
tests fail. This needs investigation ase there might be a bug masked by
the optimization
updated ontologies from OWL 2 primer

http://www.w3.org/TR/owl2-primer/
fixed wrong property type inference in HasKey parsing
Fixed a number of parsing bugs in Manchester OWL Syntax
Added targeted parsing to allow one and only one parser to be tried on a
document input source. 

Implements #80 targeted parsing of ontologies, if a bit clumsily. To be
refactored.
updated primer files. Added a test with /fixed/ primer input to assert
equivalence of the five syntaxes.
Better implementation for targeted parsing, takes into account MIME type
as well.