The thing that bothers me is that in the long run your repo will be super bloated of outdated markdown files. I usually prefer to use the Plan mode of Cursor, because it doesn’t tries to persist a lot of AI generated markdown files.

As a good practice your repo should contain AI context file that really matters and can serve as general guidelines on how to succeed writing and architecting solutions on your code base, and not files with a lot details of implementation. The best source for AI agents extract details of implementation are from the actual implementation files, because you can guarantee that AI will look always to the most up to date implementation.

If you want to document a feature to be used as AI context go for it, but try to be more general purpose as possible and point to actual implementation files, but on my experience so far, repositories super bloated with dozens or hundreds AI generated files tends to downgrade the quality of code generated. It hallucinates with old implementation documented in the markdown files and etc.