Chore/change folder names

[BenjaSanchez]

Main improvements in this PR:

This partly addresses #232 by changing folder names to be compliant with MetabolicAtlas/standard-GEM.

Note that:

• This branch should not be merged until a new release of RAVEN is out (or at least feat: exportForGit folder behaviour & import COBRA modelID RAVEN#303 is merged).
• After merging this branch, there will be conflicts with our master branch that should be handled before a new release is made.

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)

[BenjaSanchez]

@edkerk I was too quick with this one: before reviewing maybe we should first settle on the model folder issue in #232 and also merge #228 to avoid conflicts :)