Multisite: How to remove subdirectory from url

Where does your multisite installation actually live in the server directory structure? Do you have a subdomain or subdirectory type of multisite? What is the function of this /directory/ folder now?

This is a domain mapped multisite. The directory folder was used in the development environment and is not available/necessary anymore on the live site.

I should have asked what sort of links still have /directory/ in URL. But I think I know the answer. They are most likely paths that are saved in your DB. The most common example of these are image URLs, but there are many other examples.

To fix those, install and activate in the primary site, the Better Search and Replace plugin. Use it to search for offending URLs and replace them with the correct path.