obsidian-zk — Obsidian Zettelkasten MCP Server

MCP server for AI-assisted Zettelkasten in Obsidian. Luhmann numbering, typed connections, SQLite metadata cache.

Works with Claude Code — exposes tools and prompts via Model Context Protocol.

What it does

• CRUD for fleeting, literature, permanent, MOC, and project notes with proper frontmatter
• Luhmann numbering — auto-generates zk_id with alternating numbers/letters (1 → 1a → 1a1 → 1a1a)
• Connection scoring — finds related notes by shared tags, keywords, Luhmann proximity, MOC overlap
• Backlinks — incoming/outgoing link tracking with path-based resolution
• Vault analysis — unprocessed notes with age warnings, orphans, emerging theme clusters
• Quality pipeline — promote fleeting/literature → permanent, finalize with quality checks
• MCP skills — guided workflows as slash commands (/zk:capture, /zk:promote, /zk:moc, etc.)
• SQLite index — incremental indexing with single-note updates, path-based link storage

No embeddings — Claude judges semantic relevance directly in context.

Quick start

1. Install

npx obsidian-zk init

Interactive wizard:

• Detects or asks for vault path
• Creates folder structure (1-Fleeting/, 2-Literature/, 3-Permanent/, 4-MOC/, 5-Projects/)
• Copies note templates, skills, and agents into .claude/
• Creates CLAUDE.md with project instructions
• Sets up SQLite database in .zk/
• Configures MCP server in .mcp.json

2. Use

Open vault directory in Claude Code:

cd your-vault
claude

The MCP server starts automatically. Use prompts:

Command	What it does
/zk:capture	Quick fleeting note from a thought
/zk:literature	Literature note from pasted source
/zk:permanent	Atomic permanent note with auto Luhmann ID
/zk:promote	Convert fleeting/literature → permanent (single/batch)
/zk:manage	Edit/archive/delete by Luhmann number
/zk:moc	Create Map of Content — auto-pulls notes by tag
/zk:project	Create project note with tasks and deadlines
/zk:finalize	Quality-check and finalize permanent notes
/zk:tree	Visualize the Luhmann knowledge tree
/zk:review	Vault health report
/zk:daily	Morning briefing with age warnings
/zk:connect	Find and create connections for a note
/zk:reflect	Deep reflection on vault themes

3. Update

After upgrading the package:

npx obsidian-zk update

Syncs skills/agents, runs DB migrations.

How it works

Claude Code ←→ MCP Server (obsidian-zk serve) ←→ SQLite DB + Vault files
                   │
                   ├── Tools (zk_capture, zk_permanent, zk_moc, zk_backlinks, ...)
                   └── Skills (/zk:capture, /zk:promote, /zk:finalize, ...)

Architecture

Component	Choice
MCP SDK	@modelcontextprotocol/sdk (stdio transport)
Database	better-sqlite3 — single .zk/zettelkasten.db file
Semantic search	Claude itself — no embeddings infra needed
Vault I/O	Node.js fs — direct file read/write

MCP Tools

CRUD:

• zk_capture — create fleeting note
• zk_literature — create literature note
• zk_permanent — create permanent note with Luhmann ID
• zk_manage — edit frontmatter + body sections, archive, delete by ID
• zk_promote — mark fleeting/literature as processed, extract key ideas
• zk_moc — create Map of Content, auto-pull notes by tags
• zk_project — create project note with tasks/deadlines

Search & connections:

• zk_find_connections — candidates scored by tags, keywords, Luhmann proximity, MOC overlap
• zk_backlinks — incoming/outgoing links for a note (by path, title, or ID)
• zk_cluster_detect — emerging themes without MOCs

Analysis:

• zk_list — filter notes by type/status/folder
• zk_unprocessed — notes needing processing with age tracking
• zk_orphans — notes with no incoming links
• zk_finalize — quality-check permanent notes (connections, claim, evidence, confidence)
• zk_next_id — next Luhmann ID
• zk_find_by_id — resolve ID → path
• zk_tree — visualize Luhmann tree (full, subtree, or context around a note)
• zk_review — full vault health report

Index:

• zk_reindex — full vault re-scan
• zk_status — DB stats

Database & indexing

The vault is markdown files. Without a DB, every operation (find connections, list unprocessed, detect orphans) would scan and parse every .md file. The SQLite DB is a read-optimized index over the vault.

Schema:

CREATE TABLE notes (
  path TEXT PRIMARY KEY,
  title TEXT, zk_id TEXT, type TEXT, status TEXT,
  folder TEXT, tags TEXT, summary TEXT, flags TEXT,
  created TEXT, modified TEXT, content_hash TEXT
);

CREATE TABLE links (
  source TEXT, target TEXT, link_type TEXT,
  PRIMARY KEY (source, target)
);

CREATE TABLE meta (key TEXT PRIMARY KEY, value TEXT);

What it accelerates:

Operation	Without DB	With DB
Find by zk_id	Scan all files, parse YAML	Single indexed query
List unprocessed	Scan + parse + filter	WHERE status IN ('unprocessed','draft')
Find orphans	Parse all files, build link graph	LEFT JOIN links ... WHERE target IS NULL
Find connections	Parse all, compare tags/keywords pairwise	Load pre-extracted tags/summary, score in-memory
Detect clusters	Same	Group pre-extracted tags

Incremental indexing via content_hash:

1. scanVault() walks all .md files
2. Compute MD5 of each file's content
3. Compare with stored content_hash — only re-parse changed files
4. A 10K vault where 3 files changed → only 3 files re-parsed

Staleness check (ensureFresh()):

Read-only tools (list, tree, orphans) call ensureFresh() instead of full reindex():

• Compares file mtime against last_index timestamp
• If nothing changed between tool calls → zero work
• If vault was edited in Obsidian → triggers incremental reindex

Link validation:

Wikilinks ([[Note Title]]) only create a DB link if the target note exists in the notes table. Unresolvable links are skipped — no phantom entries in orphan detection or backlinks.

Write-path tools (zk_capture, zk_permanent, etc.) call indexNote() on the affected file directly — no full vault scan needed.

Zettelkasten method

Note types

Folder	Type	Atomic?	Lifecycle
1-Fleeting/	Raw thoughts	No	unprocessed → processed
2-Literature/	Source summaries	Partial	unprocessed → processed
3-Permanent/	One idea per note	Yes	draft → finalized
4-MOC/	Topic indexes	No	draft → active
5-Projects/	Active goals	No	active → completed

Luhmann numbering

1, 2, 3          — independent threads
1a, 1b            — branches from 1
1a1, 1a2          — sub-branches from 1a

Connection types

• Підтримує (Supports) — reinforces another idea
• Суперечить (Contradicts) — challenges another idea
• Розширює (Extends) — builds upon another idea
• Пов'язано (Related) — topically connected

Connection scoring

Notes are scored for connection relevance using multiple signals:

• Shared tags: +2 per tag
• Keyword overlap: +1 (4+ chars), +2 (6+ chars)
• Luhmann proximity: +7 (parent/child), +5 (siblings), +2 (cousins)
• Shared MOC: +2
• Threshold: score ≥ 2 to appear as candidate

Workflow

Thought → /zk:capture → Fleeting note
Source  → /zk:literature → Literature note
                ↓
         /zk:promote (fleeting or literature)
                ↓
         Permanent note (auto zk_id) ←→ connections
                ↓
         /zk:finalize (quality check)
                ↓
         MOC (when 3+ related notes cluster)

Use cases

Research & learning

Reading a book or paper:

> /zk:literature
> Here are my highlights from "Thinking, Fast and Slow" by Kahneman...

1. /zk:literature — paste highlights, Claude creates a structured literature note with source metadata
2. /zk:promote — extract atomic ideas into permanent notes, each with its own Luhmann ID
3. /zk:connect — Claude finds related notes in your vault and suggests typed connections

Exploring a new topic:

> /zk:capture
> Just learned that mitochondrial DNA is inherited only from the mother.
> This might connect to my notes on epigenetics.

1. /zk:capture several fleeting notes as you read/watch/listen
2. /zk:daily — review what's accumulated, see age warnings for stale notes
3. /zk:promote in batch — convert the best ideas into permanent notes
4. /zk:moc — once 3+ notes cluster around a theme, create a Map of Content

Writing & thinking

Preparing an article or essay:

> /zk:reflect
> I'm writing a blog post about decision-making under uncertainty.
> What themes in my vault are relevant?

1. /zk:reflect — Claude analyzes vault themes and surfaces unexpected connections
2. /zk:review — find orphaned notes and weak spots in your knowledge graph
3. Browse MOCs to build an outline from existing permanent notes
4. /zk:connect — strengthen the argument by finding supporting/contradicting notes

Developing an argument:

> /zk:permanent
> Claim: distributed teams outperform co-located ones when
> async communication norms are explicit.

1. /zk:permanent — write your claim as an atomic note
2. /zk:connect — Claude scores candidates and suggests supporting/contradicting links
3. /zk:tree — navigate the Luhmann tree (1 → 1a → 1a1) to build a chain of reasoning
4. /zk:finalize — quality check: does the note have evidence, confidence level, enough connections?

Daily knowledge work

Morning routine:

> /zk:daily

Claude shows unprocessed notes grouped by urgency, suggests which to promote first.

1. /zk:daily — see unprocessed notes with urgency tiers, aging warnings
2. /zk:promote — process the oldest fleeting notes first
3. /zk:connect on newly promoted notes — integrate them into the graph

After a meeting or conversation:

> /zk:capture
> Meeting with Alex: they suggested using event sourcing instead of CRUD
> for the audit log. Interesting tradeoff — immutability vs query complexity.

1. /zk:capture — dump raw thoughts quickly (title + body, no structure needed)
2. Come back later, /zk:promote — Claude helps extract the key insight into a permanent note

Project management

Tracking a goal:

> /zk:project
> Project: "Q2 API redesign". Deadline: June 30.
> Key tasks: schema migration, client SDK update, docs rewrite.
> Link to my notes on REST vs GraphQL tradeoffs.

1. /zk:project — create a project note with tasks, deadlines, and linked permanent notes
2. Link relevant permanent notes as the knowledge base for the project
3. /zk:review — track overall vault health and outstanding work

Vault maintenance

Weekly cleanup:

> /zk:review

Claude reports: 12 unprocessed notes (3 urgent), 5 orphans, 2 emerging clusters without MOCs.

1. /zk:review — full vault health report (orphans, unprocessed count, link stats)
2. /zk:finalize — batch quality-check draft permanent notes
3. /zk:moc — create MOCs for emerging clusters detected by /zk:reflect

Onboarding to an existing vault:

> /zk:reflect
> I just inherited this vault. What are the main themes and how do they connect?

1. /zk:review — get a high-level picture of vault state
2. /zk:reflect — understand major themes and how they connect
3. Browse MOCs and Luhmann trees to navigate the knowledge structure

Development

git clone https://github.com/user/obsidian-zk.git
cd obsidian-zk
npm install
npm run build       # compile TypeScript
npm run dev         # watch mode
npm test            # run tests
npm run test:coverage  # with coverage

Pre-commit hook runs tests automatically via husky.

Test locally:

# Start server against a test vault
echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}' \
  | node dist/cli/index.js serve --vault /path/to/vault

# Or configure in Claude Code
claude mcp add obsidian-zk -- node /path/to/obsidian-zk/dist/cli/index.js serve --vault .

Project structure

src/
├── cli/index.ts          # CLI: init, update, serve
├── init/
│   ├── wizard.ts         # Interactive setup
│   ├── scaffold.ts       # Copy templates, create folders
│   └── updater.ts        # Sync templates, run migrations
├── server/
│   ├── index.ts          # Stdio transport entry
│   └── server.ts         # Tool + prompt registration
├── vault/
│   ├── parser.ts         # Frontmatter, wikilinks, body
│   ├── scanner.ts        # File discovery
│   └── writer.ts         # Note creation/editing + section updates
├── db/
│   ├── schema.ts         # SQLite schema + migrations
│   └── index.ts          # DB connection, indexing, connection scoring
├── tools/                # MCP tool implementations
│   ├── capture.ts        # Fleeting notes
│   ├── literature.ts     # Literature notes
│   ├── permanent.ts      # Permanent notes (from fleeting or literature)
│   ├── manage.ts         # Edit/archive/delete/finalize
│   ├── moc.ts            # Map of Content creation
│   ├── project.ts        # Project notes
│   ├── backlinks.ts      # Incoming/outgoing link queries
│   ├── search.ts         # Connection search + cluster detection
│   ├── analysis.ts       # Unprocessed, orphans, review
│   └── index-mgmt.ts     # Reindex, status
└── luhmann.ts            # ID generation + sorting
templates/                # Copied to user vault on init
├── claude/skills/        # 13 SKILL.md files
├── claude/agents/        # zk-analyzer agent
├── vault-folders/        # Default folder structure + note templates
└── CLAUDE.md.template    # Project instructions

Requirements

• Node.js ≥ 18
• Claude Code
• Obsidian (for viewing/editing notes)

License

MIT