I have the following code in my htaccess file to remove the PHP extensions:
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^([^\.]+)$ $1.php [NC,L]
However, now I added a file in /directory/index.php and I can only access it using /directory/index instead of using just /directory/ (which now throws a 404 not found).