Delete all the index.html file "Directory access is forbidden." when using .htaccess

The files are not in a public folder, I'm protecting "application" and "CodeIgniter-3.1.9" inside a private folder that is protected by the .htaccess as suggested by the guide:

For the best security, both the system and any application folders should be placed above web root so that they are not directly accessible via a browser - https://www.codeigniter.com/user_guide/i...index.html

This comment of yours early on had me concerned and thinking you might not fully understand.

I am already using .htaccess in top folder to make all directories tree completely forbidden to anyone (i.e. "Deny from all")

To me "top folder" implied the "public" folder.