Can you guys work with Martijn so we can have a standard study representation in Github, so Arachne could pick it up smoothly? We don't want to have studies floating all over the place.
Yes, absolutely - will reach out to Martijn amd Vojtech in January to brainstorm. i would even suggest that this is exactly what ARACHNE was created for and things like study protocols and other study supporting documentation should be stored in ARACHNE to start with (not in GitHub).
Again, GitHub is a code repository, used to manage code throughout the development process. You could use it to manage documents e.g. simulate what content management systems do. But as soon as a final document (or code) is ready for publishing to the world for the purpose of conducting study - create a study in ARACHNE and upload it there.