How to organize a protection system on the site?

Question

Backend

By what means is the blocking to the site organized if a directory or file was created in the site folder?

For example, if a folder was created and it is not in the git, access to the site is blocked.
Have you met this?

Answer 1

There is a system of users and rights.
Create a user mysite, give him the rights to only read the folder with the site and write to the folder with logs, run the site from under this user.
All. Your blocking is not needed, because the site simply cannot create too much.