chore: restructure tutorials

[mihai-sysbio]

Main improvements in this PR:

This PR aims to restructure the tutorials, resolving #308.

In short, it establishes self-standing, independent tutorials (with all subfolders like userData before, including the adapter). Each tutorial also has now its own protocol.
The way the adapters are handles has been slightly tweaked.

Expected to be restructured:

• tutorial for yeast-GEM:
  • stuck as step 23, reported independently here)
  • should be the full protocol.m, with all comments
• tutorial for Human-GEM
  • using geckoLight variant
• tutorial for E.coli (@Yu-sysbio is working on this)
• blank example
  • with generic protocol.m and adapter

I hereby confirm that I have:

• Selected develop as a target branch (top left drop-down menu)

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 
Running geckoCoreFunctionTests
Done geckoCoreFunctionTests
__________

Note: In the case of multiple test runs, this post will be edited.

[ae-tafur]

I think that adding the word tutorial as a prefix inside the tutorial folder may be redundant, isn't it ? or is there a specific reason to do this ?

[mihai-sysbio]

I think that adding the word tutorial as a prefix inside the tutorial folder may be redundant, isn't it ? or is there a specific reason to do this ?

Fair point, I also hesitated about this. My reasoning was that people will likely copy one of these folders, so when they do it will be clearer what is the "tutorial" what is what they modified. I might be wrong here, we should follow what is most intuitive for the users so it's good to have other opinions.

[edkerk]

Recent changes:

• Remove blankExample, as it is replaced by startGECKOproject (see feat: a function that creates a the project structure an adapter class #312)
• Restore (and update) comments in ecYeastGEM protocol.m (as agreed upon in restructure tutorials #308)
• Run through the ecYeastGEM protocol
• Simplified ModelAdapterManager commands (most relevant: .getDefault instead of .getDefaultAdapterFromPath)

Remaining:

• ecHumanGEM tutorial with GECKO light
• ecEcoli tutorial

I suggest to have these addressed in separate PRs, so that this PR with its significant refactoring of file locations can be merged with develop. I will open two Issues for the remaining tasks.