chore: move deprecated scripts

[BenjaSanchez]

Main improvements in this PR:

Moved deprecated files to separate folder to avoid confusion. Also clarified with README's the purpose of each script/data folder.

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

[edkerk]

Do we have somewhere documented which script was used for which model version? This could be dealt with by having subfolders like deprecated/sincev8.1.0/, deprecated/sincev8.1.1 etc. Perhaps not stricly required, if we consistenly move old scripts to the deprecated folder when making a new release as soon as a particular script is no longer required, and mention this explicitly in the PR message.

[BenjaSanchez]

@edkerk thanks for your feedback!

Do we have somewhere documented which script was used for which model version?

Good point, we don't. I will document it here for all the ones that were moved in this PR:

Folder	File	Model Version
modelCuration	addiSce926changes.m	yeast 8.0.0
	fixBiomassComp.m	yeast 8.1.0
	makeFormulasCompliant.m	yeast 8.1.0
	modelCorrections.m	yeast 7.7.0
	takeOutFromFormula.m	yeast 8.1.0
	updateMetaboliteFormula.m	yeast 8.3.4
otherChanges	addSLIMErxns.m	yeast 8.1.0
	clusterBiomass.m	yeast 7.8.0
	convertYmn2FBC2.m	yeast 7.7.0

[...] if we consistenly move old scripts to the deprecated folder when making a new release as soon as a particular script is no longer required, and mention this explicitly in the PR message.

I think this solution is preferable, to avoid having a very complex sub-folder structure. We can also mention it in the commit description for all new migrations.