One way is to create another directory that lives side by side with projects , e.g. java-projects or something. Another solution could be to put your Clojure workspace inside a top top directory of your repository, e.g. clojure and then have another top directory, e.g. java , where you put your Java code (e.g. inside a projects directory). Java is of course just an example!

Thanks for the input, we independently came up with your first solution, so I think there is probably something to it.

For other interested readers: an alternative we discussed was to put an empty deps.edn into each of the non-clojure polylith projects inside of projects/. I didn't test if it worked or not but it seems like another reasonable solution