DuckVault-MCP

DuckVault-MCP v0.4.0 is a local vector and graph RAG server for Obsidian Vaults and Markdown knowledge bases. Each Vault receives an isolated DuckDB index, and all MCP sessions for that Vault share one local daemon so DuckDB, WAL, VSS, the watcher, and the embedding model have a single owner.

Quick start

Requirements:

• Python 3.11–3.14

• macOS, Linux, or Windows

• an existing directory containing Markdown files

• network access during the first init only

Install and initialize:

uv tool install mcp-duckvault
duckvault init /absolute/path/to/vault

init installs the DuckDB VSS extension, downloads intfloat/multilingual-e5-small, creates a Vault-specific database, performs the first sync and an offline search smoke test, then writes a portable MCP server entry. Its location is printed as mcp_config.

The generated entry is equivalent to:

{
  "mcpServers": {
    "duckvault": {
      "command": "duckvault",
      "args": ["serve", "/absolute/path/to/vault"]
    }
  }
}

After initialization, normal MCP startup and search use cached assets only and do not install extensions or download models.

Related MCP server: vault-graph-mcp

CLI

v0.4 uses explicit subcommands. The pre-v0.4 form duckvault VAULT_PATH is no longer accepted.

duckvault init VAULT_PATH [--non-interactive] [--json]
duckvault serve VAULT_PATH
duckvault sync VAULT_PATH [--json]
duckvault sync VAULT_PATH --dry-run [--json]
duckvault status VAULT_PATH [--json]
duckvault doctor VAULT_PATH [--json]
duckvault daemon start|stop|restart|status VAULT_PATH
duckvault migrate-legacy VAULT_PATH [--legacy-db PATH]
duckvault reindex VAULT_PATH [--json]
duckvault explain-ignore VAULT_PATH PATH [--json]
duckvault visualize VAULT_PATH [--output FILE]
duckvault --version

Normally no database path is needed. DuckVault derives one from the normalized Vault path:

~/.duckvault/
├── models/
└── vaults/<vault-id>/
    ├── vault.db
    ├── endpoint.json
    ├── owner.lock
    ├── startup.lock
    ├── daemon.log
    ├── mcp-server.json
    └── backups/

An advanced --db-path override remains available. DuckVault stores the Vault identity in every database and refuses a mismatched database before indexing or deleting anything.

Status and synchronization failures

duckvault sync /absolute/path/to/vault --json
duckvault status /absolute/path/to/vault --json

A sync reports scanned, indexed, skipped, deleted, failed, and excluded. Exit status is 0 for complete, 2 for partial success, and 1 for failure. Current file failures are retained with a stable error code and timestamp and are cleared after a successful retry. Note bodies are never written to logs or failure records.

Diagnostics

duckvault doctor /absolute/path/to/vault
duckvault doctor /absolute/path/to/vault --json

doctor checks Python, DuckDB VSS, the model cache, the database, Vault permissions, Vault identity, daemon health, watcher ownership, and offline readiness. Failed checks include a concrete repair command.

Legacy database migration

Pre-v0.4 used the shared ~/.duckvault/vault.db, which has no reliable Vault identity. DuckVault therefore does not copy its index into a new Vault:

duckvault migrate-legacy /absolute/path/to/vault

The command checkpoints and backs up the legacy DB, leaves the source intact, and rebuilds a new Vault-specific index with the current parser, graph extractor, and embedding configuration. Do not delete the old DB until the new status and search results have been verified.

Versioned schema migrations create a checkpointed backup in backups/ before running in a transaction. If the parser, model, or embedding dimension changes, rebuild the index while the daemon is stopped:

duckvault daemon stop /absolute/path/to/vault
duckvault reindex /absolute/path/to/vault --json

The replacement is built in a separate database and installed only after a complete sync. A failed rebuild leaves the original database and backup intact; status and doctor report the recovery command.

Shared daemon and recovery

duckvault serve is a small stdio MCP proxy. It connects to an authenticated loopback endpoint and starts the Vault daemon if needed. Kernel-backed owner and startup locks ensure that concurrent MCP sessions still create only one owner. All database work is serialized through that daemon.

The daemon exposes these states: starting, preparing, syncing, ready, degraded, reindex_required, and stopping. Health and status remain available while preparation or synchronization is running.

Useful recovery commands:

duckvault daemon status /absolute/path/to/vault
duckvault daemon restart /absolute/path/to/vault
duckvault doctor /absolute/path/to/vault

After SIGTERM or Ctrl+C, the daemon drains queued work, checkpoints and closes DuckDB, and removes its endpoint. After an unclean exit, kernel locks are released by the OS and the next proxy replaces stale endpoint metadata.

MCP tools

Search results include obsidian://open links. Markdown frontmatter, H1–H3 headings, Markdown/Wiki links, tags, folders, resources, citations, and OKF concept metadata are represented in the local graph.

All MCP tools return versioned structured data. Retrieval responses contain schema_version, tool, count, and items; errors expose a stable code, message, and retryable flag. Limits are bounded to 100 results, graph depth to 5, and snippets to 2,000 characters.

Exclusions and visualization

.obsidian and .trash are excluded by default. Add patterns to VAULT_PATH/.vaultignore, one per line. Current matching supports simple glob patterns but is not fully gitignore-compatible.

Preview a sync without loading the model or changing the database, and inspect why a path is excluded:

duckvault sync /absolute/path/to/vault --dry-run --json
duckvault explain-ignore /absolute/path/to/vault private/note.md --json

Markdown files larger than 10 MiB fail safely without replacing their previous index entry. Configure the limit with --max-file-size BYTES or DUCKVAULT_MAX_MARKDOWN_BYTES. File and directory symlinks are not followed; Vault-external targets are never indexed.

Stop the daemon before reading the DB for a graph export:

duckvault daemon stop /absolute/path/to/vault
duckvault visualize /absolute/path/to/vault --output duckvault-graph.html

The HTML viewer is self-contained, makes no network requests, and does not embed Markdown bodies. A versioned JSON sidecar is generated beside it.

Privacy, backup, and upgrades

• Vault contents, chunks, embeddings, graph data, and metadata are stored in plaintext DuckDB files. Anyone who can read the database can inspect them.

• DuckVault applies private POSIX permissions (0700 directories and 0600 databases/configuration) where supported. Windows ACLs remain controlled by the user account and parent directory.

• Back up the Vault and its ~/.duckvault/vaults/<vault-id>/ directory together.

• Schema and index configuration versions are stored in system_config. A changed parser/model signature marks the index for rebuilding instead of silently reusing incompatible embeddings.

• Legacy migration creates a checkpointed backup before rebuilding. A database with a newer unsupported schema is rejected rather than modified.

Development

uv sync --all-extras
uv run pytest
uv run black --check src tests .github/scripts
uv run isort --check-only src tests .github/scripts

CI runs pytest on Python 3.11–3.14 on Linux and representative macOS/Windows versions, plus a clean wheel CLI smoke test.

License

MIT. The offline viewer bundles Cytoscape.js under its included license.