Clarify naming convention for model files

[mihai-sysbio]

All model files must be named based on the repository name and versioned explicitly. Example: yeast-GEM-0.1.0.json. It must also include a release.md file that describes the release notes of the different versions of the model and the data/code used to generate the new version from the previous one. This will help standardize the model generation/ customization process and thus improve the reproducibility and maintainability.