Add support for switching reasoners

[gaurav]

JPhyloref currently uses an old version of JFact (1.2.4) as more recent versions fail to process the current Phyloreferencing ontology (owlcs/jfact#19). However, we would eventually like to be able to set the reasoner being used from the command line so that we can compare the performance between different types of reasoners. We would also like to be able to consistently output the reasoner name and version number to make automated tracking of reasoning speeds easier.

Doing this requires a minor rearchitecture of JPhyloref so that each command requests the ontology object from a central resource that reads the command line to look for reasoners and versions being specified. It also needs to keep a list of all reasoners compiled into JPhyloref and allow them to be listed from the command line.

[gaurav]

One of the alternate reasoners we should look into is the Arachne reasoner, which is rule-based, and so might be quite a bit faster than full OWL reasoners.

[gaurav]

We should also look into Fact++, which in Protege appears to be able to reason over our OWL files in less than a minute. The latest version on Maven is Fact++ 1.5.2, but Protege uses Fact++ 1.6.5, which can be downloaded as JAR files.

[gaurav]

This was implemented in #20. Closing.