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mcp-markdown-vault

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Headless semantic MCP server for Obsidian, Logseq, Dendron & any markdown vault. AST-based surgical editing, hybrid vector + TF-IDF search, zero-setup local embeddings — no app or plugins required. Stdio & SSE transport, Docker-ready.

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# 📁 Markdown Vault MCP Server

**Headless semantic [MCP](https://modelcontextprotocol.io/) 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.

[![CI / Release](https://github.com/wirux/mcp-markdown-vault/actions/workflows/release.yml/badge.svg)](https://github.com/wirux/mcp-markdown-vault/actions/workflows/release.yml)
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[![npm version](https://img.shields.io/npm/v/@wirux/mcp-markdown-vault?color=cb3837&logo=npm)](https://www.npmjs.com/package/@wirux/mcp-markdown-vault)
[![Docker](https://img.shields.io/badge/ghcr.io-mcp--markdown--vault-blue?logo=docker)](https://github.com/wirux/mcp-markdown-vault/pkgs/container/mcp-markdown-vault)
[![License: MIT](https://img.shields.io/badge/license-MIT-green.svg)](https://raw.githubusercontent.com/wirux/mcp-markdown-vault/main/LICENSE)
[![TypeScript](https://img.shields.io/badge/TypeScript-5.x-3178c6?logo=typescript&logoColor=white)](https://www.typescriptlang.org/)
[![Node.js](https://img.shields.io/badge/Node.js-%3E%3D22-339933?logo=node.js&logoColor=white)](https://nodejs.org/)
[![Tests](https://img.shields.io/badge/tests-568%20passed-brightgreen?logo=vitest&logoColor=white)](https://raw.githubusercontent.com/wirux/mcp-markdown-vault/main/)
[![mcp-markdown-vault MCP server](https://glama.ai/mcp/servers/wirux/mcp-markdown-vault/badges/score.svg)](https://glama.ai/mcp/servers/wirux/mcp-markdown-vault)

</div>

![Markdown Vault MCP Server Demo](https://raw.githubusercontent.com/wirux/mcp-markdown-vault/main/assets/demo.gif)

</div>

---

## 💡 Why this server?

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

| | Differentiator | Details |
|---|---|---|
| 🚫 | **No app or plugins required** | Most Obsidian MCP servers ([mcp-obsidian](https://github.com/MarkusPfundstein/mcp-obsidian), [obsidian-mcp-server](https://github.com/cyanheads/obsidian-mcp-server)) need Obsidian running with the Local REST API plugin. This server reads and writes `.md` files directly — point it at a folder and go. |
| 🧠 | **Built-in semantic search, zero setup** | Hybrid search: cosine-similarity vectors + TF-IDF + word proximity. Local embeddings (`@huggingface/transformers`, `all-MiniLM-L6-v2`, 384d) download on first run. No API keys, no external services. Ollama optional for higher quality. |
| 🔬 | **Surgical AST-based editing** | `remark` AST pipeline patches specific headings or block IDs without touching the rest of the file. Freeform line-range & string replace as fallback. Levenshtein fuzzy matching handles LLM typos. |
| 🔓 | **Tool-agnostic** | Obsidian vaults, Logseq graphs, Dendron workspaces, Foam, or any plain folder of `.md` files. If it's markdown, it works. |
| 📦 | **Single package, no infrastructure** | Unlike Python alternatives that need ChromaDB or other vector stores, everything runs in one Node.js process. `npx @wirux/mcp-markdown-vault` and you're running. Docker image available. |

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

</div>

---

## ✨ Features

| | Feature | Description |
|---|---|---|
| 🗂️ | **Headless vault ops** | Read, create, update, edit, delete `.md` notes with strict path traversal protection |
| 📑 | **Read by heading** | Read a single section by heading title — returns only content under that heading (up to the next same-level heading), saving context window space |
| 📦 | **Bulk read** | Read multiple files and/or heading-scoped sections in a single call — reduces MCP round-trips with per-item fault tolerance |
| 🔬 | **Surgical editing** | AST-based patching targets specific headings or block IDs — never overwrites the whole file |
| 🔍 | **Fragment retrieval** | Heading-aware chunking + TF-IDF + proximity scoring returns only relevant sections |
| 📂 | **Scoped search** | Optional directory filter for `global_search` and `semantic_search` — restrict results to specific folders to reduce noise |
| 🧠 | **Semantic search** | Hybrid vector + lexical search with background auto-indexing |
| ⚡ | **Zero-setup embeddings** | Built-in local embeddings via `@huggingface/transformers` — Ollama optional |
| 🔄 | **Workflow tracking** | Petri net state machine with contextual LLM hints |
| 🌐 | **Dual transport** | Stdio (single client) or SSE over HTTP (multi-client, Docker-friendly) |
| ✏️ | **Freeform editing** | Line-range replacement and string find/replace as AST fallback |
| 🏷️ | **Frontmatter management** | AST-based read and update of YAML frontmatter — safely manage tags, statuses, and metadata without corrupting file structure |
| 👀 | **Dry-run / diff preview** | Preview any edit operation as a unified diff without saving — set `dryRun=true` on any edit action |
| 📝 | **Templating / scaffolding** | Create new notes from template files with `{{variable}}` placeholder injection — refuses to overwrite existing files |
| 🗺️ | **Self-orienting vault context** | Assisted or manual `meta/overview.md` with host-visible `vault_scope` and live `vault://overview` context for connected agents |
| 📦 | **Batch edit** | Apply multiple edit operations in a single call — sequential execution, stops on first error, supports `dryRun`, max 50 ops |
| 🔗 | **Backlinks index** | Find all notes linking to a given path — supports wikilinks and markdown links with line numbers and context snippets |
| 🎯 | **Typo resilience** | Levenshtein-based fuzzy matching for edit operations |

---

## 🛠️ MCP Tools

| Tool | Actions | Description |
|---|---|---|
| 📁 **vault** | `list` `read` `create` `update` `delete` `stat` `create_from_template` | Full CRUD for vault notes + template scaffolding |
| ✏️ **edit** | `append` `prepend` `replace` `delete` `line_replace` `string_replace` `frontmatter_set` + `operations[]` batch mode | AST-based patching + freeform fallback + frontmatter update + batch edit (supports `dryRun` diff preview) |
| 👁️ **view** | `search` `global_search` `semantic_search` `outline` `read` `frontmatter_get` `bulk_read` `backlinks` | Fragment retrieval, cross-vault search, hybrid semantic search, read by heading, frontmatter read, bulk read, backlinks |
| 🔄 **workflow** | `status` `transition` `history` `reset` | Petri net state machine control |
| ⚙️ **system** | `status` `reindex` `overview` `overview_status` `prepare_overview` `save_overview` | Server health, indexing info, vault structure overview, assisted overview rebuild |

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

---

## 💡 Operational Guidance

### 🛠️ Safe Editing
- **`dryRun=true`**: Highly recommended before destructive operations like `delete` or `replace` with `replaceMode="section"`.
- **Heading Disambiguation**: If multiple identical headings are found, the server returns `AMBIGUOUS_HEADING_TARGET` with a list of candidates. Use `blockId` to target specific elements if headings are not unique.
- **AST vs Freeform**: Always prefer AST operations (`append`, `prepend`, `replace`, `delete`) as they are structural. Use `string_replace` only as a last resort; it requires exact literal matches including whitespace and newlines.
- **`replaceMode`**: `replace` defaults to `body` (preserves the heading, replaces content). Set `replaceMode: "section"` to replace the heading node and all its child headings.
- **`returnContent`**: Set to `section` or `file` to see the results of your edit immediately in the tool response (max 8KB).

### 🚀 Performance & Consistency
- **`bulk_read`**: Use this to read 2 or more files/sections concurrently. It is significantly faster than multiple sequential `view.read` calls.
- **Workflow State**: The `workflow` tool manages session-specific state used for contextual hints. It does **not** modify vault data or search indexes.
- **`system.reindex`**: Only use this for recovery or after making out-of-band file changes (e.g., via external scripts). Normal MCP edits automatically update backlinks and queue vector indexing.
- **`view.outline`**: Supports a `directory` parameter to get a flat list of headings across multiple files in a folder.

### 🧪 Batch Edits
- **Sequential Execution**: Operations in a batch are executed one by one. If one fails, the remaining are skipped.
- **Dry-run Asymmetry**: In `dryRun=false`, each operation sees the file state after previous operations. In `dryRun=true`, the file is never written, so sequential dependent operations (e.g., editing the same line twice) may produce different results than a live run.

---

## 🚀 Quick Start

### Prerequisites

- [Node.js](https://nodejs.org/) >= 22
- *(Optional)* [Ollama](https://ollama.com/) for higher-quality embeddings

### 📦 Install from NPM

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

Then run directly:

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

### 🔌 MCP Client Configuration

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

```json
{
  "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](https://glama.ai/mcp/servers/@wirux/mcp-markdown-vault) — no local install required.

### 🐳 Docker

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

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

Or use Docker Compose:

```bash
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)

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

---

## 🌐 Transport Modes

| Mode | Use case | How it works |
|---|---|---|
| 📡 `stdio` *(default)* | Single-client desktop apps (Claude Desktop) | Reads/writes stdin/stdout; 1:1 connection |
| 🌊 `sse` | Multi-client setups (Docker, Claude Code) | HTTP server with SSE streams; one connection per client |

**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

```bash
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:

| `OLLAMA_URL` set? | Ollama reachable? | Provider used |
|---|---|---|
| ❌ No | — | 🏠 Local (`@huggingface/transformers`, `all-MiniLM-L6-v2`, 384d) |
| ✅ Yes | ✅ Yes | 🦙 Ollama (`nomic-embed-text`, 768d) |
| ✅ Yes | ❌ No | 🏠 Local *(fallback with warning)* |

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

---

## ⚙️ Configuration

| Variable | Default | Description |
|---|---|---|
| `VAULT_PATH` | `/vault` | Markdown vault directory |
| `VAULT_CONTEXT_MODE` | `assisted` | Vault orientation mode: `assisted` (host LLM/agent calls `prepare_overview` to gather evidence, then generates prose and calls `save_overview`) or `manual` (you author `meta/overview.md` yourself and the server does not overwrite it). `auto` is a deprecated alias for `assisted`. |
| `VAULT_CONTEXT` | *(deprecated)* | Deprecated and ignored. Use `VAULT_CONTEXT_MODE` instead. |
| `MCP_TRANSPORT_TYPE` | `stdio` | `stdio` (single client) or `sse` (multi-client HTTP) |
| `PORT` | `3000` | HTTP port (SSE mode only) |
| `OLLAMA_URL` | *(unset)* | Set to enable Ollama embeddings |
| `OLLAMA_MODEL` | `nomic-embed-text` | Ollama embedding model name |
| `OLLAMA_DIMENSIONS` | `768` | Ollama embedding vector dimensions |
| `VECTOR_STORE_URL` | *(unset)* | Set to use Qdrant (e.g. `http://localhost:6333`). If unset, local persisted flat store is used. |
| `VECTOR_STORE_COLLECTION` | `markdown_vault` | Qdrant collection name when `VECTOR_STORE_URL` is set. |
| `VECTOR_STORE_RESET` | `false` | Set to `true` to auto-delete a mismatched vector index on startup and rebuild from scratch. |
| `MCP_AUTH_TOKEN` | *(unset)* | Bearer token for SSE transport auth. If set, all SSE endpoints require `Authorization: Bearer <token>`. |
| `HOST_BIND_ADDRESS` | `127.0.0.1` | Bind address for the SSE HTTP server. |
| `BODY_LIMIT_BYTES` | `1mb` | Max JSON request body size for SSE `POST /messages`. |

> **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`.

Use `assisted` mode when you want the connected host LLM/agent to generate and refresh vault context from server-provided evidence. Use `manual` mode when you want to write and maintain `meta/overview.md` yourself; in manual mode, the server creates the file if missing but does not overwrite it.

---

## 🏗️ 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](CLAUDE.md) for detailed architecture docs and [CHANGELOG.md](CHANGELOG.md) for implementation history.

---

## 🗺️ Self-Orienting Context Layer

Connected agents automatically discover **when** to query this vault and **how** to use its tools — no explicit user instructions needed.

> **Quick start:** Run the **`rebuild-overview`** MCP prompt after adding notes to your vault. This generates context that helps agents route queries to the right vault.

### How it works

The server delivers vault context through multiple mechanisms (graceful degradation across clients):

| Mechanism | When | What the agent sees |
|---|---|---|
| `instructions` field | MCP handshake | `vault_scope` + tool summary |
| MCP Resources | On-demand | `vault://overview` (stats + overview + conventions) |
| First-call priming | First tool call per session | `vault_scope` + hint to read `vault://overview` |
| Tool descriptions | Tool listing | `vault_scope` string for routing |

### Modes

| Mode | How overview is managed |
|---|---|
| `assisted` *(default)* | Host agent calls `system.prepare_overview` → generates prose → calls `system.save_overview` |
| `manual` | You author `meta/overview.md` yourself; server creates stub but never overwrites |

To rebuild in assisted mode: invoke the **`rebuild-overview`** MCP prompt, or ask your agent to call `system.prepare_overview` then `system.save_overview`.

### Vault meta files

On first startup, the server creates two files in `<VAULT_PATH>/meta/`:

| File | Purpose | Managed by |
|---|---|---|
| `meta/overview.md` | Vault description + `vault_scope` routing hint | Host agent (assisted) or you (manual) |
| `meta/contract.md` | Tool usage conventions (frontmatter schema, search hints, naming) | Created once, never overwritten |

> **Tip:** Keep `vault_scope` short and specific — it tells MCP hosts what information this vault can answer.

---

## 🚢 CI/CD & Release

Fully automated via GitHub Actions and [Semantic Release](https://semantic-release.gitbook.io/):

| Workflow | Trigger | What it does |
|---|---|---|
| **PR Check** | Pull request to `main` | Lint → Build → Test |
| **Release** | Push to `main` | Lint → Test → Semantic Release (NPM + GitHub Release) → Docker build & push to `ghcr.io` |

- Versioning follows [Conventional Commits](https://www.conventionalcommits.org/) — `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`](https://www.npmjs.com/package/@wirux/mcp-markdown-vault)
- Docker image available at [`ghcr.io/wirux/mcp-markdown-vault`](https://github.com/wirux/mcp-markdown-vault/pkgs/container/mcp-markdown-vault)

---

## 🧪 Testing

**568 tests** across 49 files, written test-first (TDD).

```bash
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](LICENSE)

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