📁 Markdown Vault MCP Server

Headless semantic MCP server for Obsidian, Logseq, Dendron, Foam, and any folder of markdown files.

npm install and point it at a folder. Hybrid search, AST editing, zero-config embeddings. No app, no plugins, no API keys.

💡 Why this server?

TL;DR — One npx command. No running app. No plugins. No vector DB. Semantic search works out of the box.

💎 Obsidian · 📓 Logseq · 🌳 Dendron · 🫧 Foam · 📂 Any .md folder

✨ Features

🛠️ MCP Tools

All tool responses include contextual hints based on the current workflow state.

🚀 Quick Start

Prerequisites

• Node.js >= 22
• (Optional) Ollama for higher-quality embeddings

📦 Install from NPM

npm install -g @wirux/mcp-markdown-vault

Then run directly:

VAULT_PATH=/path/to/your/vault markdown-vault-mcp

🔌 MCP Client Configuration

Add to your MCP client config (e.g. Claude Desktop, Claude Code):

{
  "mcpServers": {
    "markdown-vault": {
      "command": "npx",
      "args": ["-y", "@wirux/mcp-markdown-vault"],
      "env": {
        "VAULT_PATH": "/path/to/your/vault"
      }
    }
  }
}

npx -y auto-installs the package if not already present — no global install needed.

Try it in the browser: You can test this server directly at Glama Inspector — no local install required.

🐳 Docker

Pull the pre-built multi-arch image from GitHub Container Registry:

docker pull ghcr.io/wirux/mcp-markdown-vault:latest

Or use Docker Compose:

docker compose up

Edit docker-compose.yml to point at your markdown vault directory. The default compose file uses SSE transport on port 3000.

🛠️ Development (from source)

git clone https://github.com/Wirux/mcp-obsidian.git
cd mcp-obsidian
npm install
npm run build
VAULT_PATH=/path/to/your/vault node dist/index.js

🌐 Transport Modes

SSE starts an HTTP server on PORT (default 3000):

• GET /sse — establishes an SSE stream (one per client)
• POST /messages?sessionId=... — receives JSON-RPC messages

MCP_TRANSPORT_TYPE=sse PORT=3000 VAULT_PATH=/path/to/vault npx @wirux/mcp-markdown-vault

Each SSE client gets its own workflow state. Shared resources (vault, vector index, embedder) are reused across all connections.

🧠 Embedding Providers

The server selects an embedding provider automatically:

No configuration needed for local embeddings — the model downloads on first use and is cached automatically.

⚙️ Configuration

Note: When using the default local vector store, a .markdown_vault_mcp directory will be created in your vault. It's recommended to add this directory to your .gitignore.

🏗️ Architecture

Clean Architecture with strict layer separation:

src/
├── domain/           🔷 Errors, interfaces (ports), value objects
├── use-cases/        🔶 Business logic (AST, chunking, search, workflow)
├── infrastructure/   🟢 Adapters (file system, Ollama, vector store)
└── presentation/     🟣 MCP tool bindings, transport layer (stdio/SSE)

See CLAUDE.md for detailed architecture docs and CHANGELOG.md for implementation history.

🚢 CI/CD & Release

Fully automated via GitHub Actions and Semantic Release:

• Versioning follows Conventional Commits — feat: = minor, fix: = patch, feat!: / BREAKING CHANGE: = major
• Docker images are built for linux/amd64 and linux/arm64 via QEMU
• NPM package published as @wirux/mcp-markdown-vault
• Docker image available at ghcr.io/wirux/mcp-markdown-vault

🧪 Testing

318 tests across 31 files, written test-first (TDD).

npm test                                          # Run all tests
npx vitest run src/use-cases/ast-patcher.test.ts  # Single file
npm run test:watch                                # Watch mode
npm run test:coverage                             # Coverage report

Tests use real temp directories for file system operations and in-memory MCP transport for integration tests. No external services required.

🔒 Security

• 🛡️ All file paths validated through SafePath value object before any I/O
• 🚫 Blocks path traversal: ../, URL-encoded (%2e%2e), double-encoded (%252e), backslash, null bytes
• ✍️ Atomic file writes (temp file + rename) prevent partial writes
• 👤 Docker container runs as non-root user

📄 License

MIT