Accidentally added “index.php” as the installation directory!

I can’t seem to reverse this mistake and I need to manually change to where it points the installation to. I have deleted and re-uploaded the wordpress files and now have them residing in a /wordpress/ directory as opposed to the root directory. The old database that I have posts is still trying to append https://www.url.com/index.php/page-subdirectory/ in between the proper URL and the page or post names.

How do I go about manually telling it where to look for the WordPress files? Do I go into cPanel and try and do it there via MySQL editor or something?