📁 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.

| | Differentiator | Details | |---|---|---| | 🚫 | No app or plugins required | Most Obsidian MCP servers (mcp-obsidian, 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

✨ 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 >= 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-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

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 for detailed architecture docs and 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:

| 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 — 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

568 tests across 49 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