check which files are modified to make everything works (nginx config files, but I think there is one more config file for cockpit to allow nginx to be used as reverse proxy)
move them in the git repo
symlink them where they should be
(add symlinks in bootstrap_root.sh ? Also add insall cockpit, since it's becoming a first class citizen project now)
I could make a dedicated git repo, but it makes sense to me to save them in the same calvinball-website git repo.
Here are some ideas:
https://tylergaw.com/blog/how-i-manage-nginx-config/