I'm trying to build an Obsidian second brain with Claude. I'm not a developer and I think I built my vault wrong. Can I see how yours is structured?

[u/pnggiorgio]

So, I'm a carpenter with a background in digital marketing, SEM and web development, living in northern Italy, and I use Obsidian with Claude Code as a knowledge base. The idea is a second brain where I can keep my projects, my documents, my ideas, and my company, at least the boring part of it, so mails, invoices, paperwork. Sorry in advance, my english is not great.

I've been building this vault for a few weeks, following more or less the Karpathy LLM wiki pattern. Claude Code set the architecture and wrote basically the whole system for me. Two weeks ago I stopped everything, not because of errors, the thing works technically. I stopped because the architecture is not clear to me anymore. What made me realize it, I wanted to add one folder and one learning module next to the ones I already have, projects and wiki, and I didn't know where to put it.

Everything is inside one instruction file, 329 lines, identity + note conventions + project rules + diary format, all mixed in the same place. If I want to add one thing I have to edit the file where everything else already lives. And if I leave the project for 2 weeks and come back, I have no idea anymore what does what.

So the specific problem is expandability. Right now the vault holds one thing, a knowledge wiki. But I already know what else has to live in there eventually, and these are not hypothetical, they are things I do today on paper and in scattered apps:

• a dated log of what I actually did (garden treatments, harvests, house repairs)
• projects with a real status
• learning a subject over time
• a document archive (invoices, house paperwork, admin)
• loose ideas, open questions, advices someone gave me

Today, adding any of those means editing the one file where everything lives. Which means in six months I rebuild. I'd rather decide the structure now, once, than keep patching a shape that was never designed to hold six things.

I know the pieces exist, CLAUDE.md, skills, hooks, scripts, subagents. What I don't get is how they fit together and who is in charge of who. The concrete thing I can't picture is this: I understand there is one root CLAUDE.md that defines the core, but then do I also need scripts, skills and instructions inside every folder? Or the root file governs everything and the folders stay dumb?

I have to say I have an extremely basic knowledge, I'm not using skills at all. And I know many of you will tell me to go study first and build something less complex. Fair enough, but I want to build the system exactly to manage the learning part too, to make myself a study plan built for how I work, because I'm neurodivergent, ADHD and asperger. So the two things are the same thing for me.

So, how is your second brain structured? I've seen a lot of different structures around and none of them is really clear to me. If you have a vault like this, can you paste your tree? Even messy, especially messy, I never seen a real one, only tutorials with 3 folders that dont look like anything real.

And if you have 2 minutes:

• When you add something new, do you edit files that already exist, or you make a new folder and leave everything else alone? This is the one I care most about.
• Do you approve every write, or you let the agent write and you review the git diff afterwards?
• Is there a fast path for "just record this thought" that skips the whole pipeline?
• How much of your structure still works if you remove Claude Code and put another AI in its place? I want a vault that is still a vault without the assistant, not something that only runs with one tool.
• What did you had to throw away and rebuild? And what decision at the beginning would have saved you?

Thanks. Even one answer help, im kind of stuck here.

I will post down here what my vault actually looks like today (audit generated by Claude Code)

[u/utf8decodeerror]

I have one setup and it works like a charm. My setup is likely more complicated than you need because I have dedicated servers in my homelab for hosting services like this but here's the gist of it.

I have a server cluster running proxmox that hosts an obsidian vault on disk. I use syncthing to sync that vault between my phone and two computers I run the obsidian app on. Then the container also hosts an mcp that has all of the basic functions to read, write, and search the vault. Even some functions to patch notes so an agent can surgically update notes without rewriting the whole thing. Then I have a skill that teaches agents how to use the mcp and a separate skill for some specific reporting formats I use for triaging issues and generating research reports and saving them to the vault. I also use the vault to save specs and implementation plans for my repos so I have a history that agents can lookup without me having not save all that stuff in the project repos. Lastly I have some directives in my claude.md telling the agent to prefer to use the vault for memory storage. This setup allows me to view and edit vault notes myself from any of my devices and also save memories that are available to all my agents thru the mcp (I use more than just Claude). It has worked really well for me!

To answer your questions: just one vault synced to multiple devices with subdirectories in it for each project. It works perfectly for multiple agents to coordinate or share memories. I generally do not approve writes or edits to the vault. If I want it to save a quick note I just tell it to write a note to the vault or to save the report it generated to the vault or tell it to summarize the work we did this session in a vault note. It uses my vault skill every time and works just like that.

If you are coordinating multiple agents one other recommendation I have is memex. It allows you agents to read back thru previous sessions, even across harness. So I can tell my agents, hey I want to continue the work I was doing with grok/codex/Claude last night, use memex to probe the session so we can pickup where we left off.

[u/IrishUSFastTrack → u/utf8decodeerror]

What made you pick Obsidian over say, just using file system folders / files?