Dead links after upgrade

I just upgraded from EE2 to EE3 for a client and my links all have an extra index.php at the beginning of them.

http://localhost:8888index.php/about-us/news-events/ is the current one but I would like it to be http://localhost:8888/about-us/news-events/ what file or files should contain this code or how do I update it in EE3 admin? This is a universal problem for all my links so I would like to be able to update it in one place rather than override each individual link.

I just can’t seem to find the code nor do I really know what I am looking for.