chore: update COBRA

[BenjaSanchez]

Main improvements in this PR:

No content changes (.txt & .yml don't change), only the order of the bqbiol:is and bqbiol:isDescribedBy qualifiers in the .xml file due to the latest COBRA changes in their export (opencobra/cobratoolbox#1266 I think). @tpfau is this an expected change in the .xml output?

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Selected devel as a target branch (top left drop-down menu)
• If needed, asked first in the Gitter chat room about this PR

[tpfau]

Yes this is expected.
To be more precise, the Toolbox will, from now on do the following with an SBML model:
Upon reading the model, any model is bioqualifier will be converted to a isDerivedFrom qualifier. This is because the Toolbox does not read everything (e.g. annotations are just those defined by cvterms).
Upon writing, any isInstanceOf or hasPart etc modifiers will be removed if no is modifier was set.
There is a simple reason behind this:
Once we read it, the model is no longer the same, as such we don't know whether it will still has these properties. So we remove them, as inaccurate information is worse than no information (in my opinion).
If a user actively set the is modifier, we assume that he knows what he is doing and does also care about the other annotations.
There is a convenience Method addMIRIAMAnnotations added to the toolbox which can be used to add and update annotations.