The big refactor

[AlexMontgomerie]

This is what I'm working on for merging the refactor and dev branches. Unfortunately the new code structure meant that it isn't able to show differences between the existing modelling (just shows up as new files vs deleted). I've been manually inspecting the files to copy over functionality, although admittedly not too thoroughly. I reckon more test coverage on the dev branch side will help show any issues with that.