Vault Cortex

Vault Cortex is a standalone MCP server that gives any AI agent hybrid search, task queries, structured memory, and read/write access to your Obsidian vault. No plugins, no running Obsidian, no separate bridge. One Docker container, your vault folder, 26 tools + 3 guided prompts. Deploy on a VPS with Obsidian Sync and the same vault is accessible from your phone, claude.ai, or any remote MCP client, secured with OAuth 2.1.

Contents — What you get · Quick Start · How It Works · Hybrid Search · Tools · Prompts · Config · Data Integrity · Auth · Deployment

What you get

• Remote access — works from your phone, a remote server, or any MCP client via OAuth 2.1. Deploy on a VPS with Obsidian Sync for access from anywhere.

• Plugin-free — Obsidian doesn't need to be running. The server works directly with .md files on disk. Headless sync keeps the vault current.

• Hybrid search — FTS5 keyword matching + vector semantic similarity via RRF fusion, refined by cross-encoder reranking for intent-heavy queries. Keywords stay precise on exact terms and jargon; vectors find notes even when your words differ from the vault's.

• Structured memory — dated entries, section targeting, auto-initialization for AI personalization

• Task queries — Kanban-aware, vault-wide task index parsing both Tasks plugin emoji and Dataview inline-field formats. Filter by status, six date fields, priority, folder, or heading — or pull board lanes in position order.

• Link graph — backlinks, outgoing links, and orphan detection across the vault

• Obsidian-native — understands frontmatter, wikilinks, tags, headings, and daily notes

• Guided workflows — three built-in prompts for vault health, memory review, and daily reconciliation — assembled from live vault data each time

Tested across a 15-day trip through Europe. 30+ sessions from a phone, 216 tool calls, zero laptop access needed. Writes in one session were immediately available in the next, across cities and days.

Related MCP server: Vault MCP Server (mschuchard)

Quick Start

Local (2 minutes — Docker + your vault folder)

Prerequisites: Docker, Node.js >= 20.12 (only for the CLI — the server itself runs in Docker), and an Obsidian vault (or any folder of .md files).

npx vault-cortex@latest init

That's it — the CLI asks for your vault path, generates the auth token and config files, starts the server, and prints the connection details for your MCP client.

# 1. Get the quickstart files
curl -O https://raw.githubusercontent.com/aliasunder/vault-cortex/main/deploy/local/docker-compose.yml
curl -O https://raw.githubusercontent.com/aliasunder/vault-cortex/main/deploy/local/.env.example

# 2. Configure
cp .env.example .env
# Edit .env — set MCP_AUTH_TOKEN (openssl rand -hex 32) and VAULT_PATH

# 3. Start
docker compose up

Full local guide → (includes Windows setup)

Remote (access from anywhere — Docker + Obsidian Sync)

Prerequisites: a VPS with Docker, an Obsidian Sync subscription, and Node.js >= 20.12 (only for the CLI — the server itself runs in Docker).

# On your VPS:
npx vault-cortex@latest init --mode remote

That's it — the CLI walks through the public URL, Obsidian Sync token (it can run the token generator for you), and auth config, then starts the server.

# On your VPS:
mkdir -p /opt/vault-cortex && cd /opt/vault-cortex
curl -O https://raw.githubusercontent.com/aliasunder/vault-cortex/main/deploy/remote/docker-compose.yml
curl -O https://raw.githubusercontent.com/aliasunder/vault-cortex/main/deploy/remote/.env.example
cp .env.example .env
# Edit .env — set MCP_AUTH_TOKEN, PUBLIC_URL, OBSIDIAN_AUTH_TOKEN, VAULT_NAME
docker compose up -d

Full remote guide →

Connect your MCP client

Add the server URL in any MCP client — Claude Code, Claude Desktop, Cursor, OpenCode, or any other. OAuth clients open a consent page in your browser — approve with your token, and the client handles token renewal from then on. Clients without OAuth (MCP Inspector, scripts) send the token directly as an Authorization: Bearer header.

Claude Code:

claude mcp add --scope user --transport http vault-cortex http://localhost:8000/mcp   # local (or <PUBLIC_URL>/mcp)

--scope user registers the server for every project; omit it to scope it to the current directory only.

The "Add custom connector" dialog only accepts https URLs. With an https PUBLIC_URL, add it directly in the connector dialog; for a localhost server, register it in claude_desktop_config.json through the mcp-remote stdio bridge instead:

{
  "mcpServers": {
    "vault-cortex": {
      "command": "npx",
      "args": [
        "-y",
        "mcp-remote",
        "http://localhost:8000/mcp",
        "--header",
        "Authorization: Bearer <your MCP_AUTH_TOKEN>"
      ]
    }
  }
}

claude.ai (web and mobile) connects to the remote setup only — its connectors are fetched server-side and can never reach localhost.

"Remote MCP server" refers to the connection type (HTTP) — in the local setup the server still runs entirely on your machine.

See Authentication for both methods and token lifetimes.

How It Works

graph LR
    Client["MCP Client"] -->|OAuth 2.1 / Bearer| Server["MCP server"]
    Server -->|read/write| Vault[("/vault<br/>.md files")]
    Server -->|FTS5 + vector| SQLite[("SQLite\nFTS5 + sqlite-vec")]
    Sync["Obsidian Sync service"] <-->|Obsidian Sync| Vault

The search index is rebuildable derived state — FTS5 keyword tables rebuild on startup, vector embeddings persist across restarts with content-hash gating (only changed notes re-embed). A file watcher keeps both current, and queries fuse both signals via Reciprocal Rank Fusion. The sync service keeps the vault in sync with your Obsidian apps — it ships inside the same container in the :remote image variant (remote deployments only; the default :latest image is the MCP server alone).

See ARCHITECTURE.md for the full design, auth flow diagrams, and component breakdown.

Hybrid Search

Keyword search alone fails when your vocabulary doesn't match the vault's — "aspirations" won't find a note about "targets", "coworkers" won't surface your "references" file. In testing against a real vault, 30% of natural-language queries returned zero or tangential results with keywords alone. Hybrid search eliminated those misses — vectors bridge the vocabulary gap, and the reranker rescues intent-heavy queries where neither signal is strong on its own.

Hybrid search combines three ranking signals via Reciprocal Rank Fusion:

• Keywords (FTS5) stay precise on exact terms, jargon, and property values

• Vectors (sqlite-vec) bridge the vocabulary gap by matching on meaning

• Reranker (cross-encoder) refines ordering by scoring each query-document pair jointly — rescues intent-heavy queries where keywords and vectors both miss

All models run locally (~45MB total, no external API). Set EMBEDDING_ENABLED=false for keyword-only search, or RERANK_MODE=none to skip reranking for lower latency.

See ARCHITECTURE.md → Hybrid Search for model details, blend weights, and the full pipeline breakdown.

Tools (26)

Prompts (3)

Tools are model-driven — the assistant calls them. Prompts are workflows you trigger. Each one queries the search index, link graph, and memory layer at invocation time, then assembles the results with guided instructions — so the session starts grounded in your vault's actual state, not assumptions.

Prompts adapt to your configuration (MEMORY_DIR, daily-notes settings) and work for any vault out of the box. Pass max_chars to cap embedded content if your client has payload limits.

Client support: Prompts work in Claude Desktop (Chat and Cowork — via the + menu under your connector), Claude Code (slash commands), and OpenCode. Support in other clients (Cursor, Windsurf) varies — see the MCP clients matrix for the latest.

Properties

Vault Cortex indexes every property in your notes, but five get promoted treatment — dedicated columns for fast filtering, and top-level fields in every search and discovery result:

All other properties are still fully queryable — use vault_search with filters.properties for combined text + metadata queries, or vault_search_by_property for metadata-only lookups. vault_list_property_keys and vault_list_property_values discover what properties exist across your vault.

These are conventions, not requirements — Vault Cortex works with any property schema. Promoted properties just give you richer filtering and cleaner results out of the box.

Leading callouts get the same treatment. When a note's first body content is an Obsidian callout (> [!type]) — either right after frontmatter or right after the title heading — it's indexed and surfaced alongside every search and discovery result. This makes notes self-describing: an agent scanning results can see what each note is for before deciding which to read. The memory templates use > [!info] Scope of this file callouts for this, and any note in your vault can use the same pattern.

Configuration

All settings are environment variables with sensible defaults.

Smart defaults: Setting MEMORY_DIR automatically updates the defaults for PROTECTED_PATHS and ORPHAN_EXCLUDE_FOLDERS. You only set those explicitly for a fully custom list. When MEMORY_ENABLED is false, the memory layer is fully disabled — memory tools are hidden and the memory folder is not auto-created.

See templates/memory/ for memory file examples and the dated-entry design philosophy.

Data Integrity

Vault Cortex writes to personal notes — the file safety layer is built to prevent corruption, not just errors.

• Atomic writes — every file write stages to a temp file, then renames. Readers never see a partial or 0-byte note. Exclusive creates use link() (POSIX no-clobber) to close the TOCTOU window on note moves.

• Per-file mutex — concurrent MCP tool calls serialize or fail-fast per file. Moves lock the source, destination, and every backlink source as one unit.

• Path traversal blocked — resolveSafePath() resolves then prefix-checks every path. Protected-path deletion is refused after normalization. Memory file names reject separators at the boundary.

• Injection prevention — search queries are parameterized and FTS5-sanitized; prompt content is wrapped in XML data markers with closing-tag escaping to prevent tag-breakout injection.

• Container hardening — non-root user, PID 1 init (tini), no package managers in the runtime image, digest-pinned base, log rotation.

See ARCHITECTURE.md → Data Integrity for mechanism details and SECURITY.md → Runtime Hardening for the full attack-surface inventory.

Authentication

For a server with read/write access to personal notes, authentication is not optional. Vault Cortex implements the full OAuth 2.1 specification, including PKCE and refresh-token rotation. The AWS (SST) deployment adds defense-in-depth: requests are validated at two independent layers (API Gateway Lambda authorizer + Express middleware). Per BlueRock's 2026 MCP security analysis, only 8.5% of MCP servers implement OAuth; 41% have no authentication at all.

Two methods:

OAuth uses dynamic client registration — no Client ID/Secret needed. A consent page opens in your browser; enter your MCP_AUTH_TOKEN to approve. Refresh tokens have a 60-day sliding expiry (daily users never re-authenticate).

See ARCHITECTURE.md → Auth for the full flow diagram.

Deployment Options

Both paths run the same image, ghcr.io/aliasunder/vault-cortex — :latest is the MCP server alone (local), :remote bundles Obsidian Sync in the same container under s6-overlay supervision. One container means any OCI runtime works: docker run, Podman, nerdctl — Docker Compose is optional.

Cost: A remote setup needs a VPS and $5/mo for Obsidian Sync. A 2 GiB instance handles semantic search fine for a typical vault; 4 GiB adds headroom for concurrent search and larger vaults. Skip semantic search entirely to go smaller still. Local-only is free. The reference AWS deployment runs ~$18–30/mo all-in.

Development

# Run locally with hot reload
PUBLIC_URL=http://localhost:8000 MCP_AUTH_TOKEN=local-dev-token VAULT_PATH=~/Vault npm run dev:mcp

# Tests
npm test

# Full check suite
npm run prettier:check && npm run lint && npm test && npm run build

MCP Inspector — interactive browser UI for testing tools:

# Start server (terminal 1), then:
npx @modelcontextprotocol/inspector
# Enter http://localhost:8000/mcp as URL, local-dev-token as Bearer token

See CONTRIBUTING.md for the full development setup.

Companion: obsidian-vault skill

The MCP server works on its own with any client. For agents that support skills (Claude Code, Cursor, Windsurf, Cline, and 70+ others), the obsidian-vault skill adds deeper knowledge of Obsidian-flavored markdown — frontmatter conventions, callout syntax, and plugin-specific formats like Dataview, Tasks, and Kanban.

npx skills add aliasunder/agent-skills --skill obsidian-vault

Skill source →

Roadmap

Acknowledgments

Obsidian sync is powered by obsidian-headless — containerization approach inspired by @Belphemur's obsidian-headless-sync-docker. The :remote image's s6-overlay supervision scaffolding was absorbed from that project's maintained fork and now lives in this repo.

The hybrid search pipeline draws on patterns from @tobi's qmd — RRF fusion with rank bonuses, position-aware score blending for cross-encoder reranking, content-hash gating, and heading-aware chunking.

Contributing

See CONTRIBUTING.md for development setup, code conventions, and PR guidelines.

License

MIT

The :remote image bundles obsidian-headless (the ob CLI), which is proprietary — its package.json declares "license": "UNLICENSED" (© Dynalist Inc. / Obsidian). It is installed from public npm at build time; the MIT license here does not cover it, and using it requires an active Obsidian Sync subscription. The :latest (local) image contains no proprietary components.

Security

Report vulnerabilities privately — see SECURITY.md.