Literate programming is the mix of both prose and code in the same file. Emacs org-mode makes extensive use of this with its tangling and code blocks functionality.

Perhaps, a good way to document the work of agents is through literate programming. Imagine the agent not only produces code but also explanations on the rationales behind its decisions. This could be useful for reducing cognitive load when trying to understand what changes the agent has made.

Silly Business talks about this as well in their blog post.