fix: disable adding prefix 'M_' and 'R_' in exprotModel function

[haowang-bioinfo]

Main improvements in this PR:

• This PR modify exportModel function to stop adding by prefix M_ and R_ to metabolite and reactions ids, as proposed in refactor: remove prefix 'M_' and 'R_' in exprotModel/importModel functions #353

I hereby confirm that I have:

• Tested my code on my own machine
• Followed the development guidelines.
• Selected devel as a target branch
• If needed, asked first in the Gitter chat room about this PR

[edkerk]

To my opinion, importModel should then also be changed, see my comment in #353.

[edkerk]

Also, I suggest this would be part of a minor release (2.5.2 -> 2.6.0). It might break compatibility of scripts that would have relied on the identifiers having their prefix removed, and full COBRA <-> RAVEN compatibility.

[mihai-sysbio]

Very nice to have this fix in Raven. I noted a few things

• in io/exportModel.m:510 this should be updated rdf:about="#meta_R_' model.rxns{i} '"
• not compulsory: there's a reference to meta_M in doc/io/exportModel.html:391 and to meta_R in the same file on line 569
• I think @edkerk noted that there is no function that reports all SBML-invalid identifiers, which I agree should be part of this PR that solves refactor: remove prefix 'M_' and 'R_' in exprotModel/importModel functions #353 see below

[mihai-sysbio]

* [ ]  I think @edkerk noted that there is no function that reports all SBML-invalid identifiers, which I agree should be part of this PR that solves [refactor: remove prefix 'M_' and 'R_' in exprotModel/importModel functions #353](https://github.com/SysBioChalmers/RAVEN/issues/353)

On second thought, @edkerk would it be okay to resolve the concern above as a different PR, to keep PRs small and targeted? This PR will then resolve only a part of #353, which makes sense to me.

[edkerk]

• Remove line 225-231, where c_ is appended to model.comps.

[haowang-bioinfo]

there's a reference to meta_M in doc/io/exportModel.html:391 and to meta_R in the same file on line 569

the html files will be corrected by the m2html later

[mihai-sysbio]

the html files will be corrected by the m2html later

As far as I can see m2html is not meant to be run automatically, so would it make sense to run it now so that all the changes are consistently applied?

[edkerk]

We have the routine to run updateDocumentation just before making a new release (example #357), but it doesn't hurt to run it earlier already.

[edkerk]

Successful I/O of yeast-GEM.

[haowang-bioinfo]

Here I merge this since tiny progress is still progress. The ID check function and importModel will be modified in other PRs.