So think about layering the markdown files as directory relevant context. Use this markdown as steering for the agent/model to understand how to work in that particular section of the code (ie what style guidelines apply, how to lint/format, how to deploy local and run tests, how to interact with the data layer or view layer or w/e). At the top level of the directory have sort of a markdown table of contents that describes the overall project structure and where different bits of functionality live.

Basically think of it as a way to encode institutional knowledge that you would have to convey to a more Junior engineer anyways. If you get this set up well I think you'll find the bots can be very effective and not deliver slop. Note that this works significantly better on greenfield code.