So far I have three different folders in my project for three different types of md documents that I keep creating and revising together with the agent: reports, plans, and reviews

Every large feature has at least one of each file created for it in that order. I start by analysing stuff and making reports that might also contain design thinking and decisions. Once I'm satisfied we have properly analysed and thought though whatever it is we're working on then I might make a plan or just jump into implementation depending on how complex the issue is. And then I might have zero or multiple reviews of different kinds by different agents depending on how much verification I think the issue warrants.

This is my super simple worse-is-better development process. I make up what is needed on the spot.