Looking for a better approach to dev documentation during development

Collective brain needed on this one. Every time I create a feature or make a large change, markdown files in ./docs/ get created or updated. So far this has worked well, but as the project grows, new features start to supersede older ones, and the documentation ends up without any clear hierarchy.

I’m thinking about adding a ./docs/inbox/ directory, along with some kind of agent that organizes the folder structure, checks whether older features are still valid as new ones come in, and generally keeps things structured.

Are there any established approaches for this? Also, markdown on a filesystem isn’t a strict requirement.