There are still some differences between the two, and I expect some answers from Jon and Brian regarding irregularities in the ontologies.
The Pellet libraries have not yet been removed.
Make TBoxReasonerModule a module on the Application. Make the reasoner status available through the module.
Initialize it in startup_listeners.txt
Create a concrete class for PelletTBoxReasonerModule, and configure it in applicationSetup.n3
Get rid of PelletReasonerSetup.
Make it so the ExecutorService in BasicTBoxReasonerDriver uses a VitroBackgroundThread.,