merged pkb branch into master

[Chris Mungall]

This mostly affects non-core modules. A few new modules such as owl2_graph_reasoner, and owl2_lcs. Lots more documentation in multiple modules. A new application - webthea - extends ClioPatria. More on that in a future email.

This is a summary of the core module changes:

owl2_export_rdf.pl

* added owl_synchronize_to_rdf/1
- translates existing owl2_model.pl database into current rdf_db

* now exports annotationAssertion/3 facts

* fixed reify/6 to use the correct owl vocabulary

owl2_from_rdf.pl

* added translate_rdf_db/1
- translates a graph in current rdf_db instance into an owl2_model.pl set of facts.

* uses sub_atom/5 rather than sub_string/5 (yap compat)

owl2_rl_rules

* added pldoc diectives
* added hooks for owl2_reasoner.pl

Cheers
Chris