Updating notebooks using Git pull changes owner to root

If you use git pull to update the notebooks the changed files get the owner and group root:root. This makes the notebook unable to be saved. I tried correcting this locally(docker) by using the $chown --preserve[=ATTR_LIST] but that did not seem to work for some reason.

Start by inspecting the repository's Dockerfiles and the notebook update workflow, then reproduce a git pull inside the Docker environment. Trace why updated files become owned by root:root and determine the expected ownership that allows notebooks to be saved. Done means updates retain writable ownership for the notebook user.

Written by the indexing model from the issue text.