Semantic Changes.
Added (STUPIDLY) support for different numbers of MTs in the main model code. Still needed in the plotting code. Still verifying compilation and such, but should be working. This really should be done in an object oriented manner (there is an active git branch for this) but until that is finished, which will take longer, this should work, though it is NOT an acceptable long term solution.
... I'm sorry. It shouldn't have come to this. I have yet to test it, but this compiles and I suspect works. This really needs to be fixed though, this code is just asking to break on you.
updated plotting code to reflect changes
Running and plotting code appear to work after simple tests. As no logic has changed, I feel this is sufficient to warrant a push, but I will be on the lookout for any issues that arise