I have Wordpress running on my dedicated server, and I thought it would be a good idea to use Git so that I can track changes that I make over time.

I have updated a few things, mostly just little changes to CSS or commenting out some HTML from PHP pages.

Q1: Will Wordpress notice these changes and merge them into new versions of the files it installs?

A few days ago I was able to update translations and a plugin with out any problems. Today I update WP to 5.9.1 from 5.9.0. But when I now try and update translations or another plugin, it wants me to enter an FTP username/password. I don't run FTP on my server, and I don't want to either.

I now have a critical issue on the site health status:

Background updates ensure that WordPress can auto-update 
if a security update is released for the version you are currently using.

Warning The folder /var/www/html/ was detected as being under version control (.git).

Error Your installation of WordPress prompts for FTP credentials to perform updates.
(Your site is performing updates over FTP due to file ownership. Talk to your hosting company.)

I saw the warning about version control before, but the warning about FTP seems to be new.

Q2: is this normal? why has this second warning appeared after the update?

Q3: how can I fix it?