Replaced log4j with java logging, removed OWLManager references

In order to fit this as a module for OWLAPI, references to OWLManager
need to exist only in the test packages.

OWLAPI uses java logging, so replacing log4j to avoid client code 
having to set up both logging systems.
This might be reverted later, as it's not clear yet whether OWLAPI
should stick with java logging or move to a different API.
removed deprecations

IRI.getStart() has been deprecated. Replaced with a simpler idiom.
URLDecoder.decode() should pass in the intended character encoding. This
should be UTF-8.
removed Log4J from test classes and added Java logging settings
refactored owl2obo and obo2owl to separate dependency on OWLManager
ignore target and mac specific files