For the application I'm working on right now, I have tons of documentation. Every feature and even bug fixes have a TDD, FDD, Implementation Plan and/or RCA document in Markdown format. And these are grouped under logical sub folders.

I also maintain a up to date master System Architect and Design document. Oh and a master index document listing every file along with a brief overview of the file.

Its very easy to give specific contexts and reference this way. The index file really helps cut down the scanning done in a cold new session.