Synapse

Your notes. Your AI's memory.

MCP server that connects any AI client — Claude, ChatGPT, Cursor, Windsurf — to your Obsidian vault. Save anything from anywhere, ask questions across your notes, keep the knowledge base your AI reads from.

30-Second Setup

Claude Desktop

1. Open config: Mac ~/Library/Application Support/Claude/claude_desktop_config.json | Windows %APPDATA%\Claude\claude_desktop_config.json
2. Add Taproot to the mcpServers object:

{
  "mcpServers": {
    "taproot": {
      "command": "npx",
      "args": ["-y", "synapse-obsidian", "/path/to/your/obsidian-vault"]
    }
  }
}

3. Restart Claude Desktop. Taproot tools appear automatically.

Claude Code

Add to .claude/.mcp.json in your home directory:

{
  "mcpServers": {
    "taproot": {
      "command": "npx",
      "args": ["-y", "synapse-obsidian", "/path/to/your/vault"]
    }
  }
}

Claude.ai / ChatGPT / Any remote AI

Run Taproot locally and expose it with a free tunnel:

# Terminal 1: Start Taproot
npx synapse-obsidian /path/to/vault --http --port 3777

# Terminal 2: Expose it (free, no account needed)
npx cloudflared tunnel --url http://localhost:3777

Copy the tunnel URL. Add https://your-tunnel-url.trycloudflare.com/mcp as a custom MCP integration in your AI client.

Getting Started

Once connected, say:

"Help me get started with Taproot"

Taproot scans your vault and gives you three options:

• Use my existing vault — Detects your folder structure, wikilinks, naming conventions. Nothing moved or overwritten. Taproot adapts to you.
• Set up a knowledge base — Creates organized folders: sources/ for raw content, notes/ for compiled knowledge, outputs/ for query results. Best for a focused research topic.
• Custom — You tell Taproot how you want things organized.

It also asks what you'll use the vault for (research, business, academic, life OS) so it can tailor the experience.

What You Can Do

Save anything, from anywhere

"Save this article: https://example.com/interesting-post"

Fetches the page, converts to markdown, saves to your vault. Works from your phone.

Ask questions across your notes

"What do my notes say about pricing strategy?"

Searches your vault, reads relevant files, synthesizes a cited answer.

Build a compounding wiki

"Process all new articles in my vault"

Turns raw sources into summaries, concept pages, entity pages — all cross-linked with wikilinks. Every answer feeds back into the knowledge base.

Health check your notes

"Run a health check on my vault"

Finds broken links, orphan pages, missing frontmatter, stale content. Fixes what it can.

All Tools

Tool	What it does
taproot_plant	Onboarding — scans vault, presents options, configures Taproot
taproot_till	Saves your vault preferences
taproot_seed	Save content from a URL or pasted text
taproot_status	Full vault overview with suggested actions
taproot_water	Process a source into organized pages
taproot_cultivate	Find and process all unprocessed sources
taproot_harvest	Research a question across your knowledge base
taproot_prune	Health-check for broken links, orphans, gaps
taproot_sow	Scaffold a new knowledge base from scratch
garden_read	Read any file
garden_plant	Create or update any file
garden_survey	List files in vault or subdirectory
garden_forage	Full-text search
garden_measure	File counts and structure
garden_tag	Read YAML metadata from a file

How It Works

Taproot is an MCP server — an open protocol for connecting AI to tools and data. It gives your AI read/write access to your vault (and nothing else — sandboxed to the vault directory).

• Stdio (default) — For desktop AI apps (Claude Desktop, etc.)
• HTTP (--http) — For browser-based AI (Claude.ai, ChatGPT, etc.) behind Tailscale or another tunnel

Your vault is just a folder of markdown files. Taproot doesn't need Obsidian to be running — it works with any folder.

Requirements

• Node.js 18+ (check with node -v)
• An Obsidian vault or any folder of markdown files
• Any MCP-compatible AI client

License

MIT — Taproot