authz_core_module

Strange. I just checked the htaccess in /application and it's in an IfModule block, so it shouldn't have mattered whether it was installed or not.

You won't lose anything by not having the file. Instead, your htaccess in the /application and /system dirs (both) should just be "Deny from all". This just prevents web access to those dirs, which is a security measure. It won't affect your app, but prevent people from going to urls like http://yoursite.com/application/models/some_model.php and being able to execute things they shouldn't have access to via their web browser.

So these 2 files
/application/.htaccess
/system/.htaccess
should both contain only

Code:

Deny from all