If your codebase is structured like 💩, an agent will smear and replicate everywhere—all the bad patterns.
So it's always a good idea to lean into the latent space every now and then and use its computational ability to choose better names, module structure, file names, and directory structure than a human can do on their own.
I call this a janitorial Roomba task. Something like this is a great fit for a skill and can run as a background cron job or a GitHub Actions job off your trunk branch.