You tell it to update the docs: not append. I've done the same thing with a readme in the root with links to the docs. After every commit, before the push, I have my agent "update all relevant and related docs, add or remove what's needed" or something to that extent. And it works remarkably well. I also have an append only change log it's supposed to add to. Between that, good commit messages, and comprehensive testing, I've built a homebrew OS and updating it is remarkably smooth. Runs a homebrew FTP and HTTP server and can run Wolfenstein. Working on DOOM right now. Close, but sound has been difficult.
https://github.com/ESikich/smallos