chore: add standard-GEM.md

[edkerk]

Main improvements in this PR:

• Features:
  • Comply with standard-GEM. (solves fix: add missing standard-GEM file #326)

I hereby confirm that I have:

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

[mihai-sysbio]

All good!

Human-GEM has opted to have a single .deprecated folder at the top level. I'm curious why is best on a day-to-day, and if perhaps consensus can be reached (it would be simpler to have the same behaviour across repositories).

[edkerk]

To be honest, I think the best is not to have a deprecated at all, as old code & data is always available from earlier releases. But that would first require going through the current code & data to make sure removing it from coming and future releases does not break. Most likely this can indeed all be deleted. With that in mind, there shouldn't be anything added to these folders.

[mihai-sysbio]

as old code & data is always available from earlier releases

Indeed, but it's not easy to do a recursive search in all previous releases for some lines of code that one vaguely knows of. In my view, code reuse is better facilitated if the deprecated files are kept. The discussion in Human-GEM took place here SysBioChalmers/Human-GEM#190 .

[edkerk]

Thanks, very insightful!