The recommended way to use this system: Obsidian on one side, your AI agent on the other. You talk to the AI. It reads, writes, and organizes your wiki. You watch the results appear in Obsidian in real time — follow links, check the graph view, browse what's changed.
Obsidian is where you browse your wiki. You can talk to your AI directly inside Obsidian using a plugin, from a terminal alongside it, or from any AI tool you already use — Claude Code, Cursor, the Claude app, whatever you prefer.
1. Open the vault. This repo ships as a ready-to-use Obsidian vault. Open the cloned directory as a vault in Obsidian — graph colors, core plugins, and display settings are pre-configured.
2. Open your AI tool next to it. No plugin needed. Just open Claude Code, the Claude desktop app, Cursor, or ChatGPT alongside Obsidian. You talk to the AI in one window, the wiki updates in real time in the other.
That's the whole setup. Obsidian is the viewer. The AI is the writer. They don't need to be connected — they both just read and write the same folder of files.
3. Start talking. See the Quick Start for what to say first.
Already set in the shipped vault, no action needed:
| Setting | Value | Why |
|---|---|---|
| New files default location | _inbox/ |
Ctrl+N always creates in the inbox. Inbox-first without thinking. |
| Templates folder | _meta/templates/ |
Ctrl+T inserts from the included set. |
| Daily notes location | 3-Journal/ |
Daily note button creates a journal entry with the right template. |
| Attachments location | assets/ |
Images stored in a fixed directory, not scattered. |
| Graph view | Color-coded by directory | Projects (blue), Knowledge (green), Journal (purple), Private (red), Inbox (orange), System files (gray) |
| Workspace files | Gitignored | Your local layout stays private. |
All plugins here are optional. The system works without any of them.
To install community plugins: Obsidian Settings → Community plugins → Turn off restricted mode → Browse.
By default you use an AI tool (Claude Code, Claude app, Cursor, ChatGPT) in a separate window next to Obsidian. If you'd rather type to the AI inside Obsidian itself, these plugins add that:
| Plugin | What it does |
|---|---|
| Claudian | Claude Code panel inside Obsidian — runs your full CLAUDE.md session protocol |
| claude-obsidian | Claude Code with hot cache for faster context loading — same as above, faster startup |
| Terminal | Embedded terminal pane inside Obsidian — run claude directly without switching apps |
| Copilot | AI chat sidebar — works with Claude, GPT-4, and others. Note: this is a generic chat panel and does not run your CLAUDE.md session protocol — your instruction modules, training phase, and inbox behavior won't apply |
Install the Obsidian Web Clipper browser extension. See the Web Clipper Setup section below for the template.
| Plugin | What it does |
|---|---|
| Dataview | Query engine for metadata — build dashboards and filtered views |
| Kanban | Visual kanban boards backed by markdown |
| Periodic Notes | Daily/weekly/monthly notes mapped to 3-Journal/ — extends the built-in daily notes with weekly and monthly views |
Dataview caveat: This system's metadata format (**Type:** knowledge, single colon) is incompatible with Dataview's inline field syntax (**Type**:: knowledge, double colon). Dataview cannot query your existing notes as written. To use Dataview, you either need to migrate your files to double-colon syntax or switch to YAML frontmatter — both are significant changes to how the system operates. If dashboard queries are important to you, use YAML frontmatter from the start. If not, skip Dataview.
If you install Obsidian Web Clipper, import the pre-built template to drop clips straight into your inbox with the right metadata:
- Open the Web Clipper extension → click the gear icon → Templates
- Click Import and select
assets/clipper-template.jsonfrom this repo - Set it as your default template
That's it. Every clip lands in _inbox/ with the metadata standard applied.
The template adds one important field:
> Why I saved this: [fill in one sentence before closing the clipper]
Fill this in before you close the clipper — one sentence is enough. Your AI uses it at triage to decide what to do:
| What you write | What the AI does |
|---|---|
| "read later" | Leaves it in inbox, surfaces it at next session |
| "save the key points on X" | Extracts the relevant knowledge, files it, discards the raw clip |
| "relates to [project name]" | Links it to or files it under that project |
| "source for [draft name]" | Pulls relevant quotes into the draft |
| (left blank) | Asks you what you want before doing anything |
If you skip the line, your AI will ask before filing — it won't guess.
Store images locally. Bind "Download attachments for current file" to a hotkey (e.g., Ctrl+Shift+D). The vault saves attachments to assets/. This downloads remote images to that local folder, preventing broken URLs. (Tip from Karpathy's original post)
Use the graph view. As your wiki grows, the graph view becomes a map of your thinking. Color-coded directories make it easy to spot clusters and gaps.
Let the AI handle organization. Resist the urge to manually file things. Capture into _inbox/, then let your AI suggest where it goes. That's the whole point.
The vault ships with a CSS snippet (llm-wiki.css) and graph view settings pre-configured. But you need to install a theme to get the full effect.
- Open Obsidian → Settings → Appearance → Themes → Browse
- Search for Minimal and install it
- The vault's
appearance.jsonalready points to it — it activates automatically
Minimal is the most popular Obsidian theme. It has clean typography, good dark/light mode support, and a companion plugin (Minimal Theme Settings) for further customization without touching CSS.
Adapt to system theme: In Settings → Appearance → Base color scheme, set it to Adapt to system. Obsidian will follow your OS's light/dark schedule automatically.
The vault ships with llm-wiki.css in .obsidian/snippets/. It's already enabled. It does:
- Metadata card — the
**Type:**,**Summary:**, etc. block at the top of every file renders as a subtle card with an accent border, not raw bold text - Typography — readable line length (760px max), better heading hierarchy, 1.75 line height
- Tables — cleaner borders, hover highlight
- Blockquotes — styled as pull quotes with an accent bar
If you want to customize it: Settings → Appearance → CSS snippets → pencil icon next to llm-wiki.
The graph is pre-configured with colors per directory:
| Color | Directory |
|---|---|
| Blue | 1-Projects |
| Green | 2-Knowledge |
| Purple | 3-Journal |
| Red | 4-Private |
| Orange | _inbox |
| Gray | _meta, _config |
| Teal | _output, _sources |
If Obsidian resets your graph settings (it sometimes does when the vault reopens), you can restore them by running git checkout .obsidian/graph.json and restarting Obsidian.