I think the key here is “if X then Y syntax” - this seems to be quite effective at piercing through the “probably ignore this” system message by highlighting WHEN a given instruction is “highly relevant”

Yeah I don't trust any agent to follow document references consistently. I just manually add the relevant files to context every single time.

Though I know some people who have built an mcp that does exactly this: https://www.usable.dev/

It's basically a chat-bot frontend to your markdown files, with both rag and graph db indexes.

That makes sense given that it's trained on real world developers.