$ cd ~
$ mkdir root-settings-tracking
$ git init --separate-git-dir=./root-settings-tracking/.git /
# Repository now is at the home dir of the user
# while it's tracking the files from the root.
# This is so that the repository is not visible at every level in the whole system
# If we do `git status` from any directory.
# From here, we can access our git repository
$ cd /
# Change the branch name if you want
$ git branch -m BRANCH_NAME
# Understand the risks and why it needs to be done:
# https://github.com/git/git/commit/8959555cee7ec045958f9b6dd62e541affb7e7d9
$ git config --global --add safe.directory /
# We ignore every file in the system
$ echo "*" > /.gitignore
# Then we force add and track ignored files using -f
$ git add -f /home/any_file
$ git commit -m "Your message"
$ git remote add origin [YOUR_REMOTE_GIT]
$ git push