I find connecting understanding between humans and agents is one of the most important parts of the agentic development cycle, and markdown is a great way to handle that.
Not only can you point it at an entire directory, you can point it at multiple projects, quick load a project with a keyboard shortcut, and also easily see recent file that changed to help you find the 75th file your agent just wrote for you.
Recently, I've started to add a review interface where you can track changes, and add comments for your agent, and then instead of trying to do some complicated integration with an agent, it just has a copy button, and it copies all the comments, which context, and instructions for the agent how to reply.
I also find that I generate TONS of markdown junk during development, and I needed a way to handle it and keep it out of the main repository so I built this tool: