Move to CTs

[stelmo]

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[stelmo]

@exaexa Okay, this is 95% done. The docs are messy, but illustrate the general principle. Unfortunate things:

1. pruning, it would've been nice to directly delete stuff on the original models e.g. unused fluxes, genes, isozymes etc
2. right now it is not clear what order the primal values are in - so you can differentiate them, but its hard to connect a derivative with a variable
3. Where can the code be improved for maintainability etc?

[stelmo]

This is done, everything should work in the core package, docs etc will likely be very broken. Will fix soon-ish