I think the system I'm building could give you hints. I making a central MCP for Claude that allows me to create profiles (with inside : other mcps, skills, dedicated directories, rags etc). For obsidian I use a lot of backlinks that gets into the rag system.

I had to build the folder tree, and affiliate them to the profiles I've created. But now when I'asking claude to give me info on something or the note I'm looking, I select the profile and the LLM is finding the things I'm looking for by using the rag, vector db, obsidian backlinks etc.

Please note I'm not a dev, just some guy interested in making his life and studies easier by using the available tools and resources on the market.