Redesign ontologymanagerfactory and repository use

This pull request contains a monolithic patch which fully replaces the use of a single Repository and a single OWLOntologyManager with 

Both of these changes are necessary to enable performance caching and customisable reasoning, including database native reasoning. In addition, each artifact repository (as opposed to the management repository) now includes full copies of the schema ontologies that are related to it.

The multiple repositories are created and monitored using the Sesame RepositoryManager. Either LocalRepositoryManager or RemoteRepositoryManager is used depending on a configuration variable.

In addition, querying is now performed over the full set of schema ontologies that are imported by each artifact.

Reasoning is still performed by a single OWLOntologyManager for each set of schema ontologies, including synchronisation, but this can now be relaxed in a modular manner, and the fully ordered set of schema ontologies is readily available.