jFEX Bitwise Offline Software Simulation

Base code for handling jFEX Biwise Offline Software Simulation. Small eFEX bug fix. There are a few small eFEX Bitwise Offline Simulation Software bug fixes in this MR. However, the primary purpose of the MR is to introduce the base code for the jFEX equivalent simulation. Most of this code is nearly identical to the eFEX code with changes as required to run the jFEX in the configuration that it uses in firmware/hardware. As such, I hope that agreements made with the Core Software team about future code optimisations may apply here also. The jFEX algorithms are not yet in place, and support for eta > 2.5 is also not yet in place. Some of the eFEX/jFEX code may be merged in the future, however implementing base clases for both to inherit from is not logistically possible at this time as both require further enhancement before they can be re-factored safely. This MR will allow students to begin working on the algorithmic side of the jFEX simulation - while a future MR will do the same for the gFEX. Once all done, further MRs will update all three simulations to safely support Athena MT. @afaulkne @smh