Knowledge OS — Obsidian + Claude Setup Guide

A personal knowledge operating system where Obsidian is your database and Claude is your AI agent adapted and documented for GitHub.

Knowledge OS Interface

Alt text

What Is This?

This repo contains a ready-to-use vault template and setup guide for building a Knowledge OS — a local, AI-powered workspace that combines Obsidian's structured note-taking with Claude's agentic capabilities. Claude can read, write, sort, and manage your vault files directly. Everything is stored locally as plain .md files — you own your data.

Think of it as a personal operating system for your thoughts, projects, and decisions — one that gets smarter and more personalized the more you use it.

Required Tools

Tool	Purpose	Download
Obsidian	Vault / note-taking interface	obsidian.md
Claude Pro or Max	AI agent (required for CLI/tool access)	claude.ai/upgrade
BRAT (Obsidian plugin)	Installs beta plugins from GitHub	Via Obsidian → Settings → Community Plugins → search "BRAT"
Claudian (beta plugin)	Embeds Claude directly inside Obsidian	github.com/YishenTu/claudian — installed via BRAT
obsidian-skills	Skills that teach Claude how to manage your vault	github.com/kepano/obsidian-skills

Optional (for visual customization)

Tool	Purpose	Download
AnuPuccin Theme	Clean, colorful Obsidian theme	Obsidian → Settings → Appearance → Themes → search "AnuPuccin"
Style Settings	Enables Rainbow folder colors	Obsidian → Settings → Community Plugins → search "Style Settings"
Excalidraw	Whiteboard / visual notes inside Obsidian	Obsidian → Settings → Community Plugins → search "Excalidraw"

System Overview

graph TD
    A[🧠 You] -->|type commands| B[Claudian Plugin]
    B -->|runs inside| C[Obsidian Vault]
    B -->|powered by| D[Claude AI]
    D -->|reads vault skills| E[obsidian-skills]
    D -->|reads your context| F[CLAUDE.md]
    D -->|creates & edits| G[.md Notes]
    G --> H[00 Context]
    G --> I[01 Inbox]
    G --> J[02 Projects]
    G --> K[03 Areas]
    G --> L[04 Resources]
    G --> M[05 Daily Notes]

    style A fill:#7c3aed,color:#fff
    style D fill:#f59e0b,color:#fff
    style C fill:#0ea5e9,color:#fff
    style F fill:#10b981,color:#fff

Setup Flow

flowchart LR
    P1["📦 Phase 1\nInstall Obsidian\n& create vault"]
    P2["🔌 Phase 2\nInstall BRAT\n+ Claudian plugin"]
    P3["🛠 Phase 3\nInstall\nobsidian-skills"]
    P4["📄 Phase 4\nAdd CLAUDE.md\n& run onboarding"]
    P5["⚡ Phase 5\nLearn daily\nworkflows"]
    P6["🎨 Phase 6\nOptional visual\ncustomization"]

    P1 --> P2 --> P3 --> P4 --> P5 --> P6

    style P1 fill:#7c3aed,color:#fff
    style P2 fill:#6d28d9,color:#fff
    style P3 fill:#4f46e5,color:#fff
    style P4 fill:#2563eb,color:#fff
    style P5 fill:#0284c7,color:#fff
    style P6 fill:#0891b2,color:#fff

Phase 1 — Install Obsidian & Create Your Vault

Download and install Obsidian from obsidian.md.
Open Obsidian and click Create new vault.
Name your vault and choose a local folder. All notes will be stored as plain .md files in this folder — no cloud lock-in.

Why local files? Your knowledge belongs to you. Plain Markdown files are readable by any editor, portable, and future-proof.

Phase 2 — Connect Claude Inside Obsidian

Step 1: Enable Community Plugins

Open Settings (gear icon, bottom left).
Go to Community Plugins → click Turn on community plugins.

Step 2: Install BRAT

In Community Plugins, click Browse and search for "BRAT".
Install and enable it.

Step 3: Install Claudian via BRAT

Open the BRAT settings (Settings → BRAT).
Click Add Beta Plugin.
Paste this URL: https://github.com/YishenTu/claudian
Click Add Plugin and enable Claudian.

Claudian embeds Claude Code as an agent inside your vault. Claude gains full read/write/bash capabilities over your vault files — this is what makes the system agentic.

Step 4: Log in to Claude

Click the Claudian icon in the left sidebar.
Log in with your Claude Pro or Max account.
Select the model you want to use (recommended: Claude Sonnet for daily work, Opus for complex reasoning).

Step 5: Enable Yolo Mode

In the Claudian settings, enable Yolo Mode. This allows Claude to execute file commands without asking for confirmation each time — essential for smooth workflows. Only enable this if you trust the commands you're giving.

Phase 3 — Install Obsidian Skills

Skills are instruction files that teach Claude how to interact with Obsidian — how to create notes, use wikilinks, generate canvases, and use the CLI.

Via Claudian chat (recommended):

Open the Claudian chat window and paste:

Install the obsidian skills from https://github.com/kepano/obsidian-skills

Manually:

Clone the repo and copy the contents into a .claude folder at the root of your vault:

git clone https://github.com/kepano/obsidian-skills.git
# Copy the /skills folder contents into <your-vault>/.claude/skills/

Available skills after installation:

Skill	What Claude learns
`obsidian-markdown`	Wikilinks, callouts, embeds, properties
`obsidian-bases`	Creating `.base` database views
`json-canvas`	Visual canvas / mind maps
`obsidian-cli`	Vault CLI commands
`defuddle`	Web clipping — clean markdown from any URL

Phase 4 — Add the CLAUDE.md File

The CLAUDE.md file is the brain of the system. It lives in the root of your vault and tells Claude everything it needs to know: who you are, how your vault is structured, and what rules to follow.

How to set it up:

Copy the CLAUDE.md file from this repo into the root folder of your vault.
Edit it with your own information (see the template below or the included file).
Open the Claudian chat and type:
```
do the onboarding
```
Claude will read CLAUDE.md, then interview you about your background, goals, and work style to fill in the rest of your context files.

What the onboarding creates:

Claude automatically builds the following folder structure:

📁 00 Context/          ← Your profile, ICP, writing style, offering
📁 01 Inbox/            ← Raw ideas, brain dumps, unprocessed notes
📁 02 Projects/         ← Active tasks with a goal and deadline
📁 03 Areas/            ← Ongoing responsibilities (no end date)
📁 04 Resources/        ← Reference knowledge, tools, research
📁 05 Daily Notes/      ← Daily logs (format: YYYY-MM-DD.md)
📁 06 Archive/          ← Completed projects and inactive areas
📁 07 Attachments/      ← Images and media files

CLAUDE.md Template

Below is the minimal template. Customize the sections marked with ← fill in.

# Vault Context

This vault is the Obsidian Brain of **[Your Name]**.  ← fill in

## About Me

[Brief bio — who you are, what you do, your expertise.]  ← fill in

**Core Expertise:**
- [Skill 1]
- [Skill 2]
- [Skill 3]

**Work Style:** [e.g. "Creatively chaotic first, then structured."]  ← fill in

Full profile in [[00 Context/About Me]].

## Vault Structure

- **00 Context/**: Personal context profile. Read these files when creating content.
- **01 Inbox/**: Quick thoughts, brain dumps, unprocessed notes.
- **02 Projects/**: Active projects with a concrete goal and end date.
- **03 Areas/**: Ongoing areas of responsibility without an end date.
- **04 Resources/**: Reference material and knowledge repositories.
- **05 Daily Notes/**: Daily log. Format: YYYY-MM-DD.md
- **06 Archive/**: Completed projects and inactive areas.
- **07 Attachments/**: Images, PDFs, media.

## Rules for This Vault

- Use [[Wikilinks]] for connections between notes
- New notes without a clear place go in 01 Inbox/
- Keep notes atomic: one idea per note
- Daily Notes use format: YYYY-MM-DD.md
- Use YAML Frontmatter: tags, status (active/completed/paused), date
- File names: Normal capitalization with spaces (e.g. "My Note.md")
- Move completed projects to 06 Archive/ only on explicit instruction
- When I say "remember this" or "save this", save it thematically

## Session Routines

### At Session Start
1. Check 01 Inbox/ for new notes and offer to sort them

### Context on Demand
When I ask "What's happening?" or "Where did I leave off?":
Read recent Daily Notes and active projects and brief me.

### At Session End
Offer to:
1. Create a Daily Note entry with a summary
2. Save new insights as notes
3. Clean up the Inbox if needed

Phase 5 — Daily Workflows

Once set up, these are the core habits that make the system work.

The Inbox Principle

Dump everything into 01 Inbox/ during the day without thinking about structure. At the end of a session, tell Claude:

Sort the inbox

Claude reads each note and moves or reorganizes it into the right folder.

Daily Log

At the end of each day, give Claude a quick summary of what you did:

Log today: finished the client proposal, had a call with Marc, decided to pause the website project

Claude saves this as a Daily Note (05 Daily Notes/2026-04-04.md) that it can reference later.

Weekly Review

Do a weekly review based on my daily notes from this week

Claude reads your daily logs and gives you a summary of what you completed, what's open, and what to focus on next.

Remember This

Make it a habit to say "remember this" whenever you make a decision, define a rule, or learn something important:

Remember this: we're targeting B2B clients with 50-200 employees

Claude saves the information to the most relevant file in your vault.

Session Start Briefing

What's happening? / Where did I leave off?

Claude reads your recent Daily Notes and open Projects, then gives you a briefing.

Phase 6 — Visual Customization (Optional)

To recreate the look from the original video:

Theme: Settings → Appearance → Themes → search "AnuPuccin" → Install and activate.
Rainbow folders: Install the Style Settings community plugin → open Style Settings → enable Rainbow Folders (set to "Full").
Graph view colors: Open Graph View → click the settings cog → add Groups, one per folder, using path filters (e.g. path:00 Context). Assign a color to each.

Repo Structure

/
├── CLAUDE.md                    ← The AI instruction file — copy this into your vault root
├── README.md                    ← This guide
├── Obsidian brain/
│   ├── CLAUDE.md
│   ├── 00 Context/
│   ├── 01 Inbox/
│   ├── 02 Projects/
│   ├── 03 Areas/
│   ├── 04 Resources/
│   ├── 05 Daily Notes/
│   ├── 06 Archive/
│   ├── 07 Attachments/
│   └── .obsidian/
│       └── plugins/
│           ├── obsidian42-brat/     ← BRAT plugin
│           ├── claudian/            ← Claude agent plugin
│           └── obsidian-skills/     ← Vault skills for Claude

What's Missing / Known Gaps

See GAPS.md for a full list of missing pieces and improvement ideas. Summary:

No .gitignore — your vault may contain private personal data. Add one before pushing.
The original CLAUDE.md template is not publicly shared (gated behind a newsletter). This repo provides an open alternative.
No mobile setup guide (Obsidian iOS/Android + Claude mobile).
No troubleshooting section for common Claudian/BRAT issues.
No backup/sync strategy documented (Obsidian Sync, iCloud, Git).

Troubleshooting

Claudian not showing up after BRAT install → Restart Obsidian after enabling the plugin in BRAT settings.

Claude says it can't access files → Make sure your vault folder is open in Obsidian and Claudian is active. Try reopening the vault.

Skills not working → Verify the .claude/skills/ folder exists in your vault root. You may need to restart Obsidian.

Yolo Mode asks for confirmation anyway → Some commands (like deleting files) always prompt regardless of Yolo Mode. This is a safety feature.

Credits & References

Original concept & video: Julian Ivanov on YouTube
Claudian plugin: YishenTu/claudian
Obsidian Skills: kepano/obsidian-skills
BRAT plugin: TfTHacker/obsidian42-brat
Obsidian: obsidian.md
Claude: claude.ai

License

MIT — use freely, adapt, and share.