It seems unusual to have a directory under src that is not part of the namespace. I would remove the main directory if its not part of the namespace and problem solved.

Otherwise, if you keep main directory, I assume you have had to set :paths ["src/main"] configuration in the project deps.edn file to make the code run with a namespace without main (otherwise I assume it will fail if run on the command line or as a jar)

I agree that it's unusual.

:paths is already set to ["src/main"] , and the code runs fine

I'm just trying to find out if there is a way to make Cider work a little better with the existing code base

If the namespace is being added automatically when a new file is created in cider, then it's clj-refactor at work. The namespace is not added if clj-refactor is not enabled. So take a look at that project for options. Also try the clojure-mode refactoring to manually add the namespace, see if that respects the path set in the deps.edn file

Oh, that would explain why I didn't find anything in the cider docs 😅 Thank you!