How do you clean up all the tests and documentation Codex writes over time?

Over time, the documentation, test suite and logs keep growing and growing. Sometimes Codex tells me that it updated or fixed a test, but scrolling through the files, I feel like I have lots of stuff in there that I don't need anymore. How do y'all clean up your project? Do you just prompt something like "Audit my project, remove redundant tests and documentation, fix broken tests and documentation and update remaining docs and tests to match my codebase" Or what is the best way to do it?