markdown-vault-mcp
A generic markdown vault MCP server with FTS5 full-text search, semantic vector search, frontmatter-aware indexing, incremental reindexing, and non-markdown attachment support.
Documentation | Release notes | Config wizard | PyPI | Docker
Point it at a directory of Markdown files (an Obsidian vault, a docs folder, a Zettelkasten, a PARA vault) and it exposes search, read, write, and edit tools over the Model Context Protocol.
Features
- Full-text search: SQLite FTS5 with BM25 scoring, porter stemming
- Semantic search: cosine similarity over embedding vectors (FastEmbed, Ollama, or OpenAI)
- Hybrid search: Reciprocal Rank Fusion combining FTS5 and vector results
- Diversity-aware ranking: each search result list caps a single document at 2 chunks (configurable) and downweights chunks of long documents, returning sentence-scale snippets. This bounds LLM context cost per query, with full-section recovery via
read(path, section=heading) - Adaptive heading-level chunking: long sections are recursively re-split at deeper heading levels (H1 → H6) until each chunk fits a configurable word budget, improving retrieval precision on synthesising essays without manual restructuring
Upgrading. As of this release,
searchreturns query-relevant snippets in thecontentfield by default (approximately 200 words). Passsnippet_words=0to recover the prior full-chunk behaviour, or useread(path, section=heading)to fetch the full section after seeing a snippet. Documents are also re-chunked on nextreindexto honour the adaptiveMARKDOWN_VAULT_MCP_MAX_CHUNK_WORDSthreshold (default 400).
- Frontmatter-aware: indexes YAML frontmatter fields, supports required field enforcement
- OKF-aware: recognizes Open Knowledge Format bundles (an
okf_versiondeclaration in the rootindex.md) and annotates search/read results with each note's type, lifecycle status, staleness, and trust tier. Those dimensions are filterable and also nudge ranking on a detected bundle (deprecated and stale notes rank lower, and the reservedindex.md/log.mdnavigation files are demoted below real notes), and the server adds anokf_validateconformance audit plus one-shot migration transforms (okf_convert_links,okf_generate_index,okf_seed_log) for moving a vault into the format, plus a downloadable bundle export served throughcreate_download_linkwith anokf-bundlereference. Read semantics are controlled byMARKDOWN_VAULT_MCP_OKF_MODE - Incremental reindexing: hash-based change detection, only re-processes modified files; an automatic boot-time reconciliation pass picks up changes made while no server was running, and the vector index converges to the reconciled chunk set (embedding exactly the delta)
- Write operations: create, edit, append to, delete, rename documents, and move entire folder subtrees with automatic index updates
- Folder conventions: per-folder
_conventions.mdfiles carry your authoring rules, such as "reference notes stay self-contained"; the server surfaces them to LLM clients at write time via theget_conventionstool and inwrite/editresults, without interpreting them - Attachment support: read, write, delete, and list non-markdown files (PDFs, images, etc.)
- Git integration: optional auto-commit and push on every write via
GIT_ASKPASS - OIDC authentication: optional token-based auth for HTTP deployments (Authelia, Keycloak, etc.)
- MCP tools: 34 LLM-visible tools including search, read, write, edit, append, delete, rename,
move_folder, git history, manual git sync, one-time transfer links, and admin operations; plus 6 app-only tools for MCP Apps clients - MCP resources: 9 resources exposing vault configuration, statistics, tags, folders, document outlines, similar notes, recent notes, and an interactive SPA
- MCP prompts: 8 prompt templates including template-driven note creation and client-side multi-note summarization
What you can do with it
With this server mounted in Claude, you can:
- Capture a URL as a note. "Fetch , summarize as a Resource note under
3-Resources/, and link any existing notes on the topic." Claude composesfetch+search+write. - Research a topic into your vault. "Research product security regulations, compare them, and create a set of interlinked notes: one per regulation, plus a map-of-content." Claude composes web-search tools (client-side) +
writewith wikilinks. See the Research workflows guide for the full loop. - Distill today's thinking. "Summarize today's conversations into Inbox notes." Claude.ai only; uses
conversation_search+recent_chats+write. Thepara-capture-chatsprompt is the one-click version. - Find missing links. Fire the
propose-linksprompt from the+menu: it scans recently modified notes and proposes links between notes that aren't yet connected, writing them on confirmation. - Split or merge captures. "Split this Inbox note into two." / "Merge this into
<existing note>instead of duplicating." Claude composesread+write+delete.
The vault needs no external scheduler or separate capture app: it sits behind your conversations and absorbs their output.
Installation
From PyPI
pip install markdown-vault-mcp
With optional dependencies:
pip install markdown-vault-mcp[mcp] # FastMCP server
pip install markdown-vault-mcp[embeddings-api] # Ollama/OpenAI embeddings via API
pip install markdown-vault-mcp[embeddings] # FastEmbed local embeddings
pip install markdown-vault-mcp[all] # MCP + FastEmbed + API embeddings
From source
git clone https://github.com/pvliesdonk/markdown-vault-mcp.git
cd markdown-vault-mcp
uv sync --all-extras --all-groups
Docker
docker pull ghcr.io/pvliesdonk/markdown-vault-mcp:latest
To run the newest merged code instead of the newest release, use the rolling edge tag. It is rebuilt on every merge to main and carries no version identity. See Image tags for the full tag list.
docker pull ghcr.io/pvliesdonk/markdown-vault-mcp:edge
The Docker image uses [all] (MCP + FastEmbed + API embeddings). By default, semantic search works locally with FastEmbed and can switch to Ollama/OpenAI when configured. A compose.yml ships at the repo root as a starting point: copy .env.example to .env, edit, and docker compose up -d.
To attach a remote Python debugger (development only; the protocol is unauthenticated), see Remote debugging.
Linux packages (.deb / .rpm)
Download .deb or .rpm packages from the GitHub Releases page. Both install a hardened systemd unit; env configuration is sourced from /etc/markdown-vault-mcp/env (copy from the shipped /etc/markdown-vault-mcp/env.example). See the systemd deployment guide for details.
Claude Desktop (.mcpb bundle)
Download the .mcpb bundle from the GitHub Releases page. Double-click to install, or run:
mcpb install markdown-vault-mcp-<version>.mcpb
Claude Desktop opens a GUI wizard that prompts for required env vars; no manual JSON editing is needed. See Step 0 of the Claude Desktop guide for details.
Claude Code plugin
/plugin marketplace add pvliesdonk/claude-plugins
/plugin install markdown-vault-mcp@pvliesdonk
Installs the MCP server and the vault-workflow skill. See the Claude Code plugin guide for details.
Release channels
Artifacts ship on three channels. Each row lists exactly what that channel publishes.
| Channel | Version identity | Artifacts |
|---|---|---|
edge (rolling) |
None; the commit is the identity | Docker image :edge rebuilt on every merge to main; .mcpb bundle as the mcpb-bundle-edge workflow artifact; rolling unstable docs version. It leaves no git tag, GitHub release, or PyPI entry behind. |
| Pre-release | vX.Y.Z-rc.N, cut from a release/X.Y branch |
GitHub release with wheels, sdist, .mcpb bundle, and SBOM attached; Docker image under its immutable vX.Y.Z-rc.N tag only. Skips PyPI, .deb/.rpm packages, the plugin marketplace, the MCP registry, and the docs deploy. |
| Stable | vX.Y.Z |
Everything: PyPI, Docker (version tag plus ordering-aware latest / vX / vX.Y), .deb/.rpm, GitHub release assets (wheels, sdist, .mcpb bundle, SBOM), plugin marketplace and MCP registry entries (when the release is the newest stable), versioned docs with an ordering-aware latest alias. |
The PyPI split is deliberate: edge and pre-release builds never reach PyPI, where every ordinary installer would see them. A pre-release's wheels are still attached to its GitHub release and installable by URL for anyone who opts in. Rolling pointers are ordering-aware, so a patch release cut from an old release/X.Y branch never moves latest-style tags back to older content. See Release process for the full model.
Quick Start
As a library
from pathlib import Path
from markdown_vault_mcp.vault import Vault
vault = Vault(source_dir=Path("/path/to/vault"))
vault.index.build_index()
results = vault.reader.search("query text", limit=10)
As an MCP server
export MARKDOWN_VAULT_MCP_SOURCE_DIR=/path/to/vault
markdown-vault-mcp serve
With Docker Compose
-
Copy an example env file:
cp examples/obsidian-readonly.env .env -
Edit
.envto setMARKDOWN_VAULT_MCP_SOURCE_DIRto the absolute path of your vault on the host. -
Start the service:
docker compose up -d -
Check the logs:
docker compose logs -f markdown-vault-mcp
Example env files
| File | Description |
|---|---|
examples/obsidian-readonly.env |
Obsidian vault, read-only, Ollama embeddings |
examples/obsidian-readwrite.env |
Obsidian vault, read-write with git auto-commit |
examples/obsidian-oidc.env |
Obsidian vault, read-only, OIDC authentication (Authelia) |
examples/ifcraftcorpus.env |
Strict frontmatter enforcement, read-only corpus |
For reverse proxy (Traefik) and deployment setup, see the deployment guides.
Server info
The server registers a built-in get_server_info tool (via fastmcp_pvl_core.register_server_info_tool) so operators can confirm the deployed version with a single MCP call. The response carries server_name, server_version, and core_version.
Configuration
All configuration is via environment variables with the MARKDOWN_VAULT_MCP_ prefix (except embedding provider settings, which use their own conventions).
- Configuration Generator: in-browser config / Docker / systemd builder
- Configuration reference: detailed per-variable documentation with operational caveats
Domain variables
Domain environment variables use the MARKDOWN_VAULT_MCP_ prefix (except the
embedding-provider conventions OLLAMA_HOST, OPENAI_API_KEY,
OPENAI_BASE_URL, and OPENAI_EMBEDDING_MODEL, which are also honoured bare):
| Variable | Default | Required | Description |
|---|---|---|---|
OLLAMA_HOST |
http://localhost:11434 |
No | Ollama server URL for the ollama embedding provider. Bare (not MARKDOWN_VAULT_MCP_-prefixed), matching the Ollama ecosystem convention. |
OPENAI_API_KEY |
(none) | No | OpenAI API key for the openai embedding provider, and the fallback key for the summarize tool when MARKDOWN_VAULT_MCP_SUMMARIZE_OPENAI_API_KEY is unset. Bare (not MARKDOWN_VAULT_MCP_-prefixed), matching the OpenAI ecosystem convention. |
OPENAI_BASE_URL |
(none) | No | Bare fallback for MARKDOWN_VAULT_MCP_OPENAI_BASE_URL (embeddings). For the summarize tool it only routes traffic when an API key already enables the feature; it never enables summarize by itself. |
OPENAI_EMBEDDING_MODEL |
(none) | No | Bare fallback for MARKDOWN_VAULT_MCP_OPENAI_EMBEDDING_MODEL. |
MARKDOWN_VAULT_MCP_BUILD_TIMEOUT_S |
60 |
No | Maximum seconds an index-backed tool or resource waits for the FTS index to become queryable during a cold-start background build before raising IndexUnavailableError(reason="timeout"). Increase for large vaults. |
MARKDOWN_VAULT_MCP_DRAIN_TIMEOUT_S |
60 |
No | Maximum seconds an index-querying read tool waits for the IndexWriter to drain when called with wait_for_pending_writes=true. On timeout the tool answers from the current index and reports index_stale=true in the response _meta. |
MARKDOWN_VAULT_MCP_SOURCE_DIR |
/data/vault |
No | Path to the markdown vault directory. Required; the server refuses to start without it. Symbolic links inside the vault are followed on Python 3.13+. |
MARKDOWN_VAULT_MCP_READ_ONLY |
true |
No | Set to false to enable the write tools (write, edit, append, delete, rename, move_folder, fetch, git_sync, the okf_* tools, create_upload_link). git_sync also needs managed git mode; create_upload_link needs an HTTP transport. |
MARKDOWN_VAULT_MCP_DISABLE_APPS_UI |
false |
No | Hide the MCP Apps UI tools (browse_vault, show_context) from the tool listing for clients that do not render MCP Apps panels. |
MARKDOWN_VAULT_MCP_INDEX_PATH |
(none) | No | Path to the SQLite FTS5 index file; unset keeps the index in memory. Set it for persistence across restarts. |
MARKDOWN_VAULT_MCP_STATE_PATH |
(none) | No | Path to the change-tracking state file. Defaults to {SOURCE_DIR}/.markdown_vault_mcp/state.json. |
MARKDOWN_VAULT_MCP_EMBEDDINGS_PATH |
(none) | No | Path to the numpy embeddings file; required to enable semantic search. |
MARKDOWN_VAULT_MCP_INDEXED_FIELDS |
(none) | No | Comma-separated frontmatter fields promoted to the tag index for structured filtering. Changing it cold-rebuilds the index once on next startup; SEARCHABLE_FIELDS inherits this value when unset. |
MARKDOWN_VAULT_MCP_REQUIRED_FIELDS |
(none) | No | Comma-separated frontmatter fields required on every document; documents missing any are excluded from the index. |
MARKDOWN_VAULT_MCP_EXCLUDE |
(none) | No | Comma-separated glob patterns excluded from scanning (.obsidian/,.trash/). |
MARKDOWN_VAULT_MCP_TITLE_FIELD |
title |
No | Frontmatter field used as the document title (falls back to title, the first H1, then the filename). Changing it cold-rebuilds the index once on next startup. |
MARKDOWN_VAULT_MCP_SEARCHABLE_FIELDS |
(none) | No | Comma-separated frontmatter fields whose text values become keyword-searchable and enrich first-chunk embeddings. Inherits INDEXED_FIELDS when unset; the sentinel none means filterable but not searchable. Changing it cold-rebuilds the index and re-embeds once on next startup. |
MARKDOWN_VAULT_MCP_TEMPLATES_FOLDER |
_templates |
No | Relative folder where note templates live (used by the create_from_template prompt). |
MARKDOWN_VAULT_MCP_PROMPTS_FOLDER |
(none) | No | Directory of .md prompt files that extend or override built-in prompts; a relative path is resolved against SOURCE_DIR. |
MARKDOWN_VAULT_MCP_CONVENTIONS_FILE |
_conventions.md |
No | Filename of the per-folder conventions files surfaced to clients at write time (bare .md filename without glob characters). Set to none to disable folder conventions. |
MARKDOWN_VAULT_MCP_OKF_MODE |
auto |
No | OKF (Open Knowledge Format) read semantics. With auto (the default), read annotations switch on when the vault declares an OKF version in its root index.md. Use off to disable OKF semantics entirely, or on to force them for an undeclared vault. Annotations are read-only; write behavior is never affected. |
MARKDOWN_VAULT_MCP_OKF_WRITE |
false |
No | OKF (Open Knowledge Format) enforced write layer. When true on an OKF-active vault, the server stamps generated provenance on each write and clears any verified attestation when a note's content changes. It also keeps each written folder's log.md and index.md current, and exposes the okf_verify tool. Requires OKF_MODE to be auto or on (a true value with OKF_MODE=off is a config error). Off by default. |
MARKDOWN_VAULT_MCP_OKF_VERIFY |
elicit |
No | How the okf_verify tool attributes a human review. This applies only when OKF_WRITE is on, which gates the tool. With elicit (the default), okf_verify asks the human to confirm the review through an MCP elicitation and records the attestation only on an affirmative reply. It fails closed when the client cannot elicit or the human declines, so a model that holds the human's token cannot self-attest. Use trust-auth to attribute to the authenticated caller with no confirmation (safe only when the sole caller is a human-driven UI), or off to hide the tool so attestation happens through external tooling. A non-default value with OKF_WRITE off is a config error. |
MARKDOWN_VAULT_MCP_ATTACHMENT_EXTENSIONS |
(none) | No | Comma-separated allowed attachment extensions without the dot (such as pdf,png,jpg); use * to allow every non-markdown file. Unset selects the built-in allowlist. |
MARKDOWN_VAULT_MCP_MAX_ATTACHMENT_SIZE_MB |
1.0 |
No | Maximum attachment size in MB returned by read / accepted by write; 0 disables the limit. |
MARKDOWN_VAULT_MCP_MAX_NOTE_READ_BYTES |
262144 |
No | Maximum bytes returned by a full-document read of a note; use read(path, section=…) for partial reads. 0 disables the limit. |
MARKDOWN_VAULT_MCP_CHUNKS_PER_FILE |
2 |
No | Maximum chunks returned per document in search results. |
MARKDOWN_VAULT_MCP_SNIPPET_WORDS |
200 |
No | Width of the snippet window (words) in search results; 0 returns full chunk content. |
MARKDOWN_VAULT_MCP_LENGTH_DOWNWEIGHT_ALPHA |
0.25 |
No | Down-weights longer chunks in ranking: score / (1 + alpha * log(chunk_count)). |
MARKDOWN_VAULT_MCP_MAX_CHUNK_WORDS |
400 |
No | Word cap per chunk; the adaptive chunker splits at deeper heading levels, then paragraph/word boundaries, to respect it. Match it to the embedding model's context. A reindex applies a new value. |
MARKDOWN_VAULT_MCP_MAX_CHUNK_CHARS |
(none) | No | Character cap enforced alongside MAX_CHUNK_WORDS to bound token-dense chunks. Unset derives min(1500, model context * 2.8). Set a positive value for an exact cap, or -1 to scale with the model's full context (can exhaust memory on long-context models). A reindex applies a new value. |
MARKDOWN_VAULT_MCP_CHUNK_OVERLAP_WORDS |
40 |
No | Words of overlap between adjacent budget-split fragments of the same heading section (0 disables). A reindex applies a new value. |
MARKDOWN_VAULT_MCP_FOLDER_WEIGHTS |
(none) | No | Folder-prefix score multipliers (prefix:weight pairs, comma-separated, weights > 0) applied to all search modes; the deepest matching prefix wins (sessions:0.5 demotes sessions/**). |
MARKDOWN_VAULT_MCP_FTS_WEIGHTS |
(none) | No | Per-column BM25 weights (column:weight pairs, comma-separated, weights >= 0) for keyword ranking. Columns: path, title, folder, heading, content, summary. |
MARKDOWN_VAULT_MCP_EMBEDDING_PROVIDER |
(none) | No | Embedding provider: openai, ollama, or fastembed. Unset auto-detects from the environment. |
MARKDOWN_VAULT_MCP_OLLAMA_MODEL |
nomic-embed-text |
No | Ollama embedding model name. |
MARKDOWN_VAULT_MCP_OLLAMA_CPU_ONLY |
false |
No | Force Ollama to embed on CPU only. |
MARKDOWN_VAULT_MCP_OPENAI_BASE_URL |
https://api.openai.com/v1 |
No | OpenAI-compatible API base URL for embeddings; the bare OPENAI_BASE_URL is honoured as a fallback. |
MARKDOWN_VAULT_MCP_OPENAI_EMBEDDING_MODEL |
text-embedding-3-small |
No | OpenAI-compatible embedding model name; the bare OPENAI_EMBEDDING_MODEL is honoured as a fallback. |
MARKDOWN_VAULT_MCP_FASTEMBED_MODEL |
BAAI/bge-small-en-v1.5 |
No | FastEmbed model name. |
MARKDOWN_VAULT_MCP_FASTEMBED_CACHE_DIR |
(none) | No | FastEmbed model cache directory (in Docker, stored under /data/state/fastembed). |
MARKDOWN_VAULT_MCP_EMBED_CONTEXT |
false |
No | Enrich embedding input with the note title, chunk heading, and (first chunk) searchable-field values. Flipping it re-embeds the whole vault once on next startup. |
MARKDOWN_VAULT_MCP_EMBED_TIMEOUT_S |
30.0 |
No | Per-request wall-clock budget in seconds for a single embedding HTTP call (OpenAI/Ollama). The local FastEmbed backend runs in-process with no network call and ignores this. CPU-only or large-model workloads may need 60-120 s; raise this if batches time out. |
MARKDOWN_VAULT_MCP_EMBEDDING_BATCH_SIZE |
4 |
No | Number of chunks sent per embedding request. Smaller batches shorten each request (useful under a tight timeout on slow models) at the cost of more round-trips. |
MARKDOWN_VAULT_MCP_GIT_TOKEN |
(none) | No | Token/password for HTTPS git auth; remotes must be HTTPS when set. |
MARKDOWN_VAULT_MCP_GIT_REPO_URL |
(none) | No | HTTPS remote URL for managed git mode: the server clones into an empty SOURCE_DIR on startup (or validates an existing origin) and enables the pull loop, auto-commit, and deferred push. |
MARKDOWN_VAULT_MCP_GIT_USERNAME |
x-access-token |
No | Username for HTTPS git auth prompts (x-access-token for GitHub, oauth2 for GitLab, the account name for Bitbucket). |
MARKDOWN_VAULT_MCP_GIT_PULL_INTERVAL_S |
600 |
No | Seconds between git fetch + fast-forward update attempts; 0 disables periodic pull. |
MARKDOWN_VAULT_MCP_GIT_PUSH_DELAY_S |
30.0 |
No | Seconds of write-idle time before pushing; 0 pushes only on shutdown. |
MARKDOWN_VAULT_MCP_GIT_COMMIT_NAME |
markdown-vault-mcp |
No | Git committer name for auto-commits; set this in Docker where git config user.name is empty. |
MARKDOWN_VAULT_MCP_GIT_COMMIT_EMAIL |
noreply@markdown-vault-mcp |
No | Git committer email for auto-commits. |
MARKDOWN_VAULT_MCP_GIT_COMMIT_NAME_CLAIM |
(none) | No | OIDC claim key used as the commit author name (such as name); overrides GIT_COMMIT_NAME per request when an OIDC token is present. |
MARKDOWN_VAULT_MCP_GIT_COMMIT_EMAIL_CLAIM |
(none) | No | OIDC claim key used as the commit author email (such as email); overrides GIT_COMMIT_EMAIL per request when an OIDC token is present. |
MARKDOWN_VAULT_MCP_GIT_LFS |
true |
No | Run git lfs pull on startup to fetch LFS-tracked attachments; set to false for repos without LFS. |
MARKDOWN_VAULT_MCP_FILE_WATCHER |
true |
No | Watch the vault for external filesystem changes; auto-disabled when git pull or the webhook is active. Requires the file-watcher extra. |
MARKDOWN_VAULT_MCP_FILE_WATCHER_DEBOUNCE_S |
2.0 |
No | Seconds of quiet after the last filesystem event before reindexing. |
MARKDOWN_VAULT_MCP_FILE_WATCHER_ROOT_FLOOR |
true |
No | Keep the non-recursive watch on the vault root; set false to register zero source-dir-rooted FSEvents streams (avoids repeated macOS access prompts on a home-rooted vault) at the cost of root-level files relying on scans. |
MARKDOWN_VAULT_MCP_GITHUB_WEBHOOK_SECRET |
(none) | No | Shared secret for the GitHub push-event webhook; when set, mounts POST /github-webhook on HTTP/SSE transports to trigger an immediate pull + reindex on push events. |
MARKDOWN_VAULT_MCP_SUMMARIZE_PROVIDER |
(none) | No | Summarization backend (only openai is recognised). Unset auto-detects: the backend activates when credentials or an explicit endpoint are present. |
MARKDOWN_VAULT_MCP_SUMMARIZE_OPENAI_API_KEY |
(none) | No | API key for the OpenAI-compatible summarize endpoint; the bare OPENAI_API_KEY is honoured as a fallback. Unset works for keyless local endpoints (Ollama). |
MARKDOWN_VAULT_MCP_SUMMARIZE_OPENAI_BASE_URL |
(none) | No | OpenAI-compatible endpoint base URL for the summarize tool; setting it enables the tool even without an API key. The bare OPENAI_BASE_URL routes traffic only when a key already enables the feature. |
MARKDOWN_VAULT_MCP_SUMMARIZE_OPENAI_MODEL |
gpt-5-mini |
No | Chat model id used for summaries. |
MARKDOWN_VAULT_MCP_SUMMARIZE_MAX_TOKENS |
8192 |
No | Upper bound on generated tokens per summarize call; on reasoning models this budget also covers internal reasoning tokens. |
MARKDOWN_VAULT_MCP_SUMMARIZE_MAX_NOTES |
50 |
No | Cap on the number of notes summarised in one call (subtree expansion truncates to this many). |
MARKDOWN_VAULT_MCP_SUMMARIZE_MAX_INPUT_CHARS |
200000 |
No | Aggregate cap on note characters sent to the model in one call; excess is truncated with a flag on the result. |
MARKDOWN_VAULT_MCP_SUMMARIZE_TIMEOUT |
120.0 |
No | Per-request wall-clock budget in seconds for a single summarize backend call; keep it below the MCP client's request timeout so the server-side error wins the race. |
MARKDOWN_VAULT_MCP_TRANSFER_TTL_DEFAULT_S |
3600.0 |
No | Link lifetime in seconds when the caller requests no explicit TTL. |
MARKDOWN_VAULT_MCP_TRANSFER_TTL_MAX_S |
86400.0 |
No | Ceiling in seconds a caller-requested link TTL is clamped to. |
MARKDOWN_VAULT_MCP_TRANSFER_GRACE_TTL_S |
60.0 |
No | Post-success grace window in seconds: a served token's TTL shrinks to this so a stalled transfer can retry within it. |
MARKDOWN_VAULT_MCP_TRANSFER_LEASE_S |
60.0 |
No | Crashed-handler reclaim window in seconds for an in-flight reservation. |
MARKDOWN_VAULT_MCP_TRANSFER_MAX_UPLOAD_BYTES |
104857600 |
No | Maximum size in bytes of a single upload. |
MARKDOWN_VAULT_MCP_JOBS_SOFT_DEADLINE_S |
25.0 |
No | Seconds a long-running tool call may run in the foreground before it is promoted to a background job and a job handle is returned instead. |
MARKDOWN_VAULT_MCP_JOBS_RESULT_TTL_S |
3600.0 |
No | Seconds a background-job record (working or finished) is retained for polling before it expires from the store. |
MARKDOWN_VAULT_MCP_JOBS_MAX_PER_SUBJECT |
256 |
No | Maximum live background jobs per calling subject; further promotions are rejected until older records expire. |
Domain-config fields are composed inside src/markdown_vault_mcp/config.py between the CONFIG-FIELDS-START / CONFIG-FIELDS-END sentinels; env reads go through fastmcp_pvl_core.env(_ENV_PREFIX, "SUFFIX", default) so naming stays consistent, and field invariants go in __post_init__ between the CONFIG-VALIDATE-START / CONFIG-VALIDATE-END sentinels. Each field's metadata help and tags generate the table above directly, so keep them accurate and complete. See the configuration reference for the detailed prose documentation of every variable.
Core settings
| Variable | Default | Description |
|---|---|---|
MARKDOWN_VAULT_MCP_KV_STORE_URL |
file:///data/state |
Persistent-state backend URL shared by every pvl-core subsystem that needs state. memory:// is in-process and lost on restart; file:///path persists on one server; redis://, dynamodb:// and mongodb:// each need their matching extra. When unset, defaults to file:///data/state (the volume family Docker images mount), or to memory://; with a warning; on a host where that directory is not usable. |
FASTMCP_LOG_LEVEL |
INFO |
Log level for FastMCP internals and app loggers (DEBUG / INFO / WARNING / ERROR / CRITICAL). The -v CLI flag overrides to DEBUG. |
FASTMCP_ENABLE_RICH_LOGGING |
true |
Set false for plain or structured JSON log output. |
Search and embeddings
The chunker's character cap (
MARKDOWN_VAULT_MCP_MAX_CHUNK_CHARS) is derived from the embedding model's context length, so changing the embedding model re-chunks the FTS index (not just the embeddings) and triggers an automatic cold rebuild of the index on the next startup. The defaults stay memory-light (BAAI/bge-small-en-v1.5for FastEmbed,nomic-embed-textfor Ollama); long-context models, such asnomic-ai/nomic-embed-text-v1.5(8192 tokens) for FastEmbed orbge-m3:latestfor Ollama, are opt-in and need substantially more RAM/VRAM during indexing.
Git integration
Git integration has three modes:
- Managed mode (
MARKDOWN_VAULT_MCP_GIT_REPO_URLset): server owns repo setup. On startup it clones intoSOURCE_DIRwhen empty, or validates existingorigin. Pull loop + auto-commit + deferred push are enabled. - Unmanaged / commit-only mode (no
GIT_REPO_URL): writes are committed to a local git repo ifSOURCE_DIRis already a git checkout. The server neither pulls nor pushes. - No-git mode: if
SOURCE_DIRis not a git repo, git callbacks are no-ops.
When token auth is used (MARKDOWN_VAULT_MCP_GIT_TOKEN), remotes must be HTTPS.
SSH remotes (such as [email protected]:owner/repo.git) are rejected with a startup error.
Fix with: git -C /path/to/vault remote set-url origin https://github.com/owner/repo.git
Backward compatibility: MARKDOWN_VAULT_MCP_GIT_TOKEN without GIT_REPO_URL still works (legacy mode) but logs a deprecation warning.
File Watcher
Requires the watchdog optional extra: pip install 'markdown-vault-mcp[file-watcher]'. Automatically disabled when GIT_PULL_INTERVAL_S > 0 or GITHUB_WEBHOOK_SECRET is set. The watcher scopes one recursive watch per non-excluded top-level directory (not a single recursive watch on the root), so excluded directories are never registered and content under a deliberately watched dot-directory delivers its own edits. See docs/configuration.md for details.
Attachments
Non-markdown file support. See Attachments for details.
Bearer token authentication
Simple static token auth for HTTP deployments. Set a single env var; clients must send Authorization: Bearer <token>.
| Variable | Required | Description |
|---|---|---|
MARKDOWN_VAULT_MCP_BEARER_TOKEN |
Yes | Static bearer token; any non-empty string enables auth |
OIDC authentication
Full OAuth 2.1 authentication for HTTP deployments. OIDC activates when all four required variables are set. See Authentication for setup details.
Multi-auth: If both
BEARER_TOKENand all OIDC variables are set, the server accepts either credential: a valid bearer token or a valid OIDC session. This is useful when different clients use different auth flows (such as Claude web via OIDC and Claude Code via bearer token).
| Variable | Required | Description |
|---|---|---|
MARKDOWN_VAULT_MCP_BASE_URL |
Yes | Public base URL of the server (such as https://mcp.example.com; include prefix if mounted under subpath, such as https://mcp.example.com/vault). Used for OIDC auth and to auto-compute the MCP Apps domain. |
MARKDOWN_VAULT_MCP_OIDC_CONFIG_URL |
Yes | OIDC discovery endpoint (such as https://auth.example.com/.well-known/openid-configuration) |
MARKDOWN_VAULT_MCP_OIDC_CLIENT_ID |
Yes | OIDC client ID registered with your provider |
MARKDOWN_VAULT_MCP_OIDC_CLIENT_SECRET |
Yes | OIDC client secret |
MARKDOWN_VAULT_MCP_OIDC_JWT_SIGNING_KEY |
No | JWT signing key. When unset, derived deterministically from the OIDC client secret, so tokens survive restarts; rotating the secret invalidates issued tokens. Set explicitly (generate with openssl rand -hex 32) to decouple token validity from secret rotation |
MARKDOWN_VAULT_MCP_OIDC_AUDIENCE |
No | Expected JWT audience claim; leave unset if your provider does not set one |
MARKDOWN_VAULT_MCP_OIDC_REQUIRED_SCOPES |
No | Comma-separated required scopes; default openid |
MARKDOWN_VAULT_MCP_OIDC_VERIFY_ACCESS_TOKEN |
No | Set true to verify the upstream access token as a JWT instead of the id token. Only needed when your provider issues JWT access tokens and you require audience-claim validation on that token. Default: verify the id token (works with all providers, including opaque-token issuers like Authelia) |
CLI Reference
markdown-vault-mcp <command> [options]
serve
Start the MCP server.
markdown-vault-mcp serve [--transport {stdio|sse|http}] [--host HOST] [--port PORT] [--http-path PATH]
| Flag | Default | Description |
|---|---|---|
--transport |
stdio |
MCP transport: stdio (stdin/stdout, default), sse (Server-Sent Events), http (streamable-HTTP). Use http for Docker with a reverse proxy or when OIDC is enabled. |
--host |
127.0.0.1 |
Bind host for the http transport (ignored for stdio and sse); pass 0.0.0.0 to bind all interfaces inside Docker |
--port |
8000 |
Port for the http transport (ignored for stdio and sse) |
--http-path (alias --path) |
env MARKDOWN_VAULT_MCP_HTTP_PATH or /mcp |
MCP HTTP path for http transport; useful for reverse-proxy subpath mounting (such as /vault/mcp). The legacy --path spelling is still accepted. |
Reverse Proxy Subpath Mounts
By default, HTTP transport serves MCP on /mcp. You can run it under a subpath:
markdown-vault-mcp serve --transport http --http-path /vault/mcp
Equivalent env-based config:
MARKDOWN_VAULT_MCP_HTTP_PATH=/vault/mcp
For reverse proxies, you can either:
- Keep app path at
/mcpand use proxy rewrite/strip-prefix middleware. - Set app path directly to the public path (
/vault/mcp) and route without rewrite.
When OIDC is enabled under a subpath, the configuration is different: the subpath goes in BASE_URL only, and HTTP_PATH stays at /mcp. See OIDC subpath deployments.
Then your redirect URI is:
https://mcp.example.com/vault/auth/callback
index
Build the full-text search index.
markdown-vault-mcp index [--source-dir PATH] [--index-path PATH] [--force]
search
Search the vault from the CLI.
markdown-vault-mcp search <query> [-n LIMIT] [-m {keyword|semantic|hybrid}] [--folder PATH] [--json]
reindex
Incrementally reindex the vault (only processes changed files). When semantic search is configured, the vector index is converged to the updated chunk set: exactly the changed documents are re-embedded and orphaned vectors dropped, never the whole corpus.
markdown-vault-mcp reindex [--source-dir PATH] [--index-path PATH]
MCP Tools
| Tool | Description |
|---|---|
search |
Hybrid full-text + semantic search with optional frontmatter filters |
read |
Read a document or attachment by relative path |
write |
Create or overwrite a document or attachment |
edit |
Replace text in a document: exact match, line-range, or scoped match with normalized fallback |
append |
Append text to the end of a note without reading it first (optional create_if_missing) |
delete |
Delete a document or attachment and its index entries |
rename |
Rename/move a document or attachment, updating all index entries; pass update_links=true to also rewrite backlinks in other notes |
move_folder |
Move an entire folder subtree to a new prefix, rewriting all vault links that point into the moved subtree in one call |
list_documents |
List indexed documents; pass include_attachments=true to also list non-markdown files |
list_folders |
List all folder paths in the vault |
list_tags |
List all unique frontmatter tag values |
reindex |
Incrementally reindex files changed outside the server; fast runs answer inline with real counts, slow runs promote to a job (get_job_result) |
stats |
Get vault statistics (document count, chunk count, link health metrics, etc.) |
build_embeddings |
Build or rebuild vector embeddings for semantic search; fast convergence answers inline, slow builds promote to a job (get_job_result) |
embeddings_status |
Check embedding provider and index status |
get_index_status |
Check background FTS build state (queryable / building / failed) |
get_backlinks |
Find all documents that link to a given document |
get_outlinks |
Find all links from a document, with existence check |
get_broken_links |
Find all links pointing to non-existent documents |
get_similar |
Find semantically similar notes by document path |
| `get_to |
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