Manually merged in @joncison's edits from 2016-05-10

Except for random reordering of relations and other bits by Protégé.

Assumingly fixes issues #130, #131, #132, #134, #136, #141, #142, #145, #146, #150, #151, #152, #156, #157, #158, #159, #160, #168, #169.
And tackles or solves issues #143, #144, #147, #148.

Merging done 'manually' difference-by-difference in Altova XMLSpy 2016 sp1 (x64).