Obsidian Company Brain: The Folder Structure I Use

A Folder Replaced My Tech Stack

I've tried ClickUp, Notion, Trello, Asana, Monday, and a half-dozen CRMs. Every single one did too much, charged per seat, and owned my data. In 2023 I moved everything into Obsidian — a local-first markdown editor with no cloud dependency. Two years later, it runs my entire agency.

40+ active clients. Sales pipeline. Proposals. Processes. Finance. Blog strategy. Product specs. Client one-pagers. All of it lives in a single vault on my machine. Backed up to Git. Queryable by AI via Cortex. No subscription. No API rate limits. No vendor lock-in.

That vault is my company brain. This post is the exact file structure I use, why each folder exists, and how I turned it into a deployable product for clients.

What Is an Obsidian Company Brain?

An Obsidian company brain is a single vault that holds how your business actually runs — clients, processes, pricing, decisions — as linked markdown files that any person or AI can read cold. It is a second brain with a different owner: it belongs to the business, not to one person's thinking.

That difference changes what goes in it:

• A second brain captures ideas, reading notes, and half-formed thoughts. It only has to make sense to you.
• A company brain captures decisions, procedures, and the current state of every client. It has to make sense to someone who wasn't in the room — a new hire, a contractor, or an AI session starting from zero.

The test is simple: if you disappeared for two weeks, could someone open the vault and keep the business running? If the answer lives only in your head, your email, or a SaaS tool you can't export from, it isn't in the brain yet. Everything below is built to pass that test.

Why Obsidian Over Everything Else

The pitch for every SaaS tool is the same: "We'll organize your business." The reality is also the same: you spend more time configuring the tool than doing the work. Then the pricing changes, the API breaks, or they get acquired and sunset your favorite feature.

Obsidian is different because:

• Local-first. Your data is markdown files on your machine. Not in someone else's database.
• No lock-in. Every note is a .md file. Move it anywhere. Read it with anything.
• Wikilinks. Double-bracket links between notes create a knowledge graph. Your notes connect to each other, and those connections become queryable.
• Zero recurring cost. The app is free. Sync is optional. Plugins are community-built.
• AI-compatible. Markdown is what LLMs read best. Your vault is already structured for AI retrieval — you just need something to walk the graph.

The File Structure

Here's the actual folder structure I use. Not a template — the real thing. Every folder earned its place by being used daily, weekly, or monthly. If it wasn't pulling its weight, I archived it.

_CONTEXT.md          # One file to give AI full company context
CLAUDE.md            # Instructions for Claude Code sessions
Tags Index.md        # Tag taxonomy — keeps tagging consistent

Company/             # Mission, model, positioning, site overview
Clients/             # One-pager per client (status, stack, notes)
Sales/               # Pipeline, objection handling, pitch decks
Proposals/           # Drafts, sent, signed — mirrors CRM states
Finance/             # Pricing, invoices, retainers, projections
Processes/           # SOPs, delivery runbooks, checklists
Product/             # Highlander, Doon, Signal, Cortex, Gateway specs
Docs/                # Symlinked app documentation (read-only)

Marketing/           # Content calendar, outreach, campaigns
Blogs/               # Blog strategy, drafts, ideas
SEO/                 # Keyword research, ranking tracking
Brand/               # Brand kit, colors, voice guidelines

Security/            # Threat intel, audit reports, incident logs
Research/            # Industry research, competitive analysis
Templates/           # Reusable templates (proposals, reports, briefs)

Notes/               # Inbox — tag and move when stable
Archive/             # Deprecated notes — never delete, just archive
      

A few things to notice:

• _CONTEXT.md is the most important file. It's a single document that gives any AI tool (Claude Code, Cortex, or a new team member) full company context in one read. Who we are, what we sell, how we work, and where to find everything. Every vault needs this.
• Notes/ is an inbox, not a folder. New thoughts go here. When they're stable, they get tagged and moved to a permanent folder. This prevents the "where does this go?" paralysis.
• Docs/ is symlinked. App documentation lives in the code repos. I symlink it into the vault so I can search it alongside business notes without duplicating files.
• No plugins required. This structure works with zero community plugins. Wikilinks, tags, and folders are all you need.

The _CONTEXT.md Pattern

This is the single most valuable file in the vault. It answers every question an AI (or a human) would ask in the first 5 minutes of looking at your business:

• Who & what — company name, founder, model, client count, core product
• Positioning — the one-line pitch and key differentiators
• What we sell — offerings table with price anchors
• Vault entry points — read-order for full context (this file first, then dashboard, then structure)
• Key files by task — "If you need to do X, go to Y"
• Vault rules — what's read-only, what's an inbox, how tags work

When I open a Claude Code session, the first thing it reads is _CONTEXT.md. Cold start time drops from 10 minutes of explanation to zero. The AI knows who I am, what I'm building, and where to find everything.

Wikilinks Are the Architecture

The folder structure organizes your vault spatially. Wikilinks organize it semantically. When a client note links to a process, and that process links to a template, and that template links to a product spec — you've built a knowledge graph without installing anything.

This is what makes it AI-queryable. Araptus Cortex walks these wikilinks as a graph. Ask Claude about a client's project, and Araptus Cortex follows the links from the client note → to the process → to the product spec — delivering structured context at configurable depth.

No embeddings. No vector database. No cloud. Just the connections you already made between your notes.

Jake Van Clief puts the principle better than I can: "If you structure the data right, one model can become as many agents as you need as it navigates that data." He and David McDermott formalised it as a folder-based method with numbered stages and a contract for each one. I break down Van Clief's folder structure here. A company brain is the knowledge half of the same idea. The other half is what happens when several agents work at once, which is where parallel AI coding agents collide.

The same principle scales past your own vault. If a folder full of plain markdown is the most legible thing you can hand an AI, then the most legible thing you can hand someone else's AI is a business that publishes its structure the same way — which is why araptus.com ships an agent-readable manifest external assistants can actually call.

Turning It Into a Product

After running my business from this vault for two years, the question became obvious: why don't my clients have this?

Most small businesses run on a combination of sticky notes, email threads, Google Docs they can never find, and a CRM they barely use. Their institutional knowledge lives in the founder's head. When they're sick, on vacation, or scaling — that knowledge is unavailable.

So I productized the vault into a Client Business Brain — the deployable version of this is Araptus Cortex, our knowledge engine — same structure, adapted for their industry. We deploy it in a single Claude Code session on their machine:

• Vault Core — Company/, Processes/, Templates/, dashboards, _CONTEXT.md
• Blog Module — Blogs/ folder with templates and a /blog skill
• Press Release Module — newswire-format templates and a /press-release skill
• Marketing Module — content calendar, campaign planning
• Finance Module — invoice tracking, pricing summary
• Sales Module — pipeline, pitch materials, objection handling

Each module creates the folders, seeds the templates, and installs Claude Code skills so the client can generate blog posts, press releases, and reports from their own context — using their own business data.

They keep everything. We leave nothing behind except a working system. Their data never leaves their machine.

Principles That Make It Work

• One vault, one truth. Don't split across multiple vaults. One vault with clear folder boundaries beats three vaults you can't cross-reference.
• Inbox → permanent. Notes/ is the inbox. Everything starts there. When it's stable, tag it and move it to the right folder. This prevents decision paralysis on capture.
• Archive, never delete. Old notes aren't trash — they're history. Move deprecated content to Archive/. You'll search it someday.
• Tags in frontmatter. Use YAML frontmatter tags, not inline hashtags. They're queryable, filterable, and machine-readable.
• _CONTEXT.md is non-negotiable. Every vault needs a single file that tells a new reader (human or AI) everything they need to know. Update it monthly.
• Symlink, don't copy. If documentation lives in a code repo, symlink it into the vault. One source of truth, searchable from both contexts.
• Earn your folders. Don't create folders speculatively. A folder earns its place by having 3+ notes in it. Until then, it lives in Notes/.

Getting Started

You don't need to build the whole structure on day one. Start with three folders and one file:

1. _CONTEXT.md — Write down who you are, what you do, and what matters. One page.
2. Notes/ — Your inbox. Everything goes here first.
3. Company/ — Move your mission, positioning, and team info here when it stabilizes.
4. Processes/ — The first time you explain how you do something, write it down here. It's now an SOP.

The vault grows with your business. In six months you'll have a system that no SaaS tool can replicate — because it's built from your actual workflows, not someone else's template.

Obsidian Company Brain: Common Questions

Do I need plugins to build a company brain in Obsidian?

No. Folders, wikilinks and YAML frontmatter tags are enough. Plugins can help later, but every one you add is something that can break or be abandoned. The structure should work without them.

How is an Obsidian company brain different from Notion?

Notion stores your pages in its database, on its servers, behind its pricing. An Obsidian vault is a folder of plain markdown files on your own machine. You can back it up with Git, read it with any editor, and hand it to any AI model. Nothing has to be exported, because it was never locked in.

Can AI tools read an Obsidian vault?

Yes, and that's the main reason to build one. Markdown is the format language models read best. Start with a single context file that says who you are, what you sell and where things live, and any AI session can pick up your business in one read.

Where should I start?

Small: one context file, an inbox folder, and a folder for processes. Write down a process the second time you explain it. The rest of the structure grows as the business uses it.

Can my whole team share one company brain?

Not comfortably in Obsidian alone. A vault lives on one machine, so a teammate who needs it gets files emailed or a git lesson. We're building the team version, Araptus Shared Brain, a shared second brain your people and your AI work in together, and it's open for early access.