added a config option called reasoner.incremental.allowed to
allow/disallow incremental mode via configuration. unit tests updated.
allowing/disallowing incremental mode from the Protege's GUI. Do not
reset the taxonomies when incremental mode is disallowed (a taxonomy can
still be queried). Placing the code which reads the config and sets the
reasoner's internal fields into the setConfigurationOptions method in
Reasoner (the factory calls this method after instantiation); it is also
called from Protege to change properties in an existing reasoner
instance.
updating the random walk-based incremental ABox tests to also track
assertions as changing axioms. a few changes to benchmarking (class
renamings and a new test to eval both TBox and ABox incremental
reasoning)
fixed a potential deadlock in TaxonomyCleaning: removeInstanceNode
should not be called while sync'ing on the parent type node
a listener, some wrappers, and some code re-org to receive notifications
inside the reasoner if the indexer indexes some axiom which can't be
incorporated incrementally (untested)
new transitivity axioms should also abandon incremental updates
a javadoc tweak
removing the logged error which should be an error at all
dynamic incremental mode switching, getting rid of some not needed axiom
loaders, some refactoring. some tests fail
a test showing that role need to be re-saturated even if no role axiom
was added, just because some roles could be new
if the role isn't saturated yet, getSubProperties must still include
itself
some commented block removed
a small test to check that we unlink contexts correctly
resolving the bug with removing the context which is the first in the
linked list stored in the saturation state
using an explicit boolean flag to indicate that some non-incremental
change was processed during the change loading stage
Merge branch 'master' into feature/incremental-taxonomy

Conflicts:
	elk-reasoner/src/test/java/org/semanticweb/elk/reasoner/incremental/LowLevelIncrementalABoxTest.java

Further Taxonomy refactoring
further taxonomy refactoring
Merge branch 'master' into feature/incremental-taxonomy