remove dependency of deep business logic on git

[Panaetius]

A lot of places in our code look like https://github.com/SwissDataScienceCenter/renku-python/blob/develop/renku/core/management/datasets.py#L443 where we directly add files to git. But this methods should not have to care about git, instead returning the files as a result and the caller can take care of committing them.

Find all places with this and similar dependencies on git and refactor them accordingly.