obsidian-zk 0.1.0

package/README.md

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+# 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](https://claude.ai/code) — exposes tools and prompts via [Model Context Protocol](https://modelcontextprotocol.io/).
+
+## What it does
+
+- **CRUD** for fleeting, literature, and permanent notes with proper frontmatter
+- **Luhmann numbering** — auto-generates `zk_id` with alternating numbers/letters (`1 → 1a → 1a1 → 1a1a`)
+- **Connection search** — finds related notes by shared tags, keywords, link proximity
+- **Vault analysis** — unprocessed notes, orphans, emerging theme clusters
+- **MCP prompts** — guided workflows as slash commands (`/zk:capture`, `/zk:promote`, etc.)
+- **SQLite index** — fast metadata queries without scanning files every time
+
+No embeddings — Claude judges semantic relevance directly in context.
+
+## Quick start
+
+### 1. Install
+
+```bash
+npx obsidian-zk init
+```
+
+Interactive wizard:
+- Detects or asks for vault path
+- Creates folder structure (`1-Fleeting/`, `2-Literature/`, `3-Permanent/`, etc.)
+- 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:
+
+```bash
+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 → permanent |
+| `/zk:manage` | Edit/archive/delete by Luhmann number |
+| `/zk:review` | Vault health report |
+| `/zk:daily` | Morning briefing |
+| `/zk:connect` | Find and create connections for a note |
+| `/zk:reflect` | Deep reflection on vault themes |
+
+### 3. Update
+
+After upgrading the package:
+
+```bash
+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_find_connections, ...)
+                   └── Prompts (/zk:capture, /zk:promote, /zk:review, ...)
+```
+
+### 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/archive/delete by ID
+- `zk_promote` — mark fleeting as processed
+
+**Search & connections:**
+- `zk_find_connections` — candidates by tags + links + keywords
+- `zk_cluster_detect` — emerging themes without MOCs
+
+**Analysis:**
+- `zk_list` — filter notes by type/status/folder
+- `zk_unprocessed` — notes needing processing
+- `zk_orphans` — notes with no incoming links
+- `zk_next_id` — next Luhmann ID
+- `zk_find_by_id` — resolve ID → path
+- `zk_list_ids` — all numbered notes
+- `zk_review` — full vault health report
+
+**Index:**
+- `zk_reindex` — full vault re-scan
+- `zk_status` — DB stats
+
+### Database schema
+
+```sql
+CREATE TABLE notes (
+  path TEXT PRIMARY KEY,
+  title TEXT, zk_id TEXT, type TEXT, status TEXT,
+  folder TEXT, tags TEXT, summary TEXT,
+  created TEXT, modified TEXT, content_hash TEXT
+);
+
+CREATE TABLE links (
+  source TEXT, target TEXT, link_type TEXT,
+  PRIMARY KEY (source, target)
+);
+```
+
+Incremental indexing — compares `content_hash`, only updates changed files.
+
+## 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 | — |
+| `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
+
+### Workflow
+
+```
+Thought → /zk:capture → Fleeting note
+Source  → /zk:literature → Literature note
+                ↓
+         /zk:promote (or /zk:permanent)
+                ↓
+         Permanent note (auto zk_id) ←→ connections
+                ↓
+         MOC (when 3+ related notes cluster)
+```
+
+## Development
+
+```bash
+git clone https://github.com/user/obsidian-zk.git
+cd obsidian-zk
+npm install
+npm run build       # compile TypeScript
+npm run dev         # watch mode
+```
+
+Test locally:
+
+```bash
+# 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
+├── db/
+│   ├── schema.ts         # SQLite schema
+│   └── index.ts          # DB connection + indexing
+├── tools/                # MCP tool implementations
+└── luhmann.ts            # ID generation + sorting
+templates/                # Copied to user vault on init
+├── claude/skills/        # 9 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](https://claude.ai/code)
+- [Obsidian](https://obsidian.md/) (for viewing/editing notes)
+
+## License
+
+MIT

package/dist/cli/index.d.ts

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+#!/usr/bin/env node
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/cli/index.d.ts.map

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package/dist/cli/index.js

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+#!/usr/bin/env node
+/**
+ * CLI entry: init, update, serve subcommands.
+ */
+import { resolve } from "node:path";
+const args = process.argv.slice(2);
+const command = args[0];
+async function main() {
+    switch (command) {
+        case "init": {
+            const { runWizard } = await import("../init/wizard.js");
+            const { scaffold } = await import("../init/scaffold.js");
+            const answers = await runWizard(process.cwd());
+            scaffold(answers);
+            break;
+        }
+        case "update": {
+            const { update } = await import("../init/updater.js");
+            const vaultFlag = args.indexOf("--vault");
+            const vaultPath = vaultFlag >= 0 ? args[vaultFlag + 1] : ".";
+            update(vaultPath);
+            break;
+        }
+        case "serve": {
+            const { startServer } = await import("../server/index.js");
+            const vaultFlag = args.indexOf("--vault");
+            const vaultPath = vaultFlag >= 0 ? args[vaultFlag + 1] : ".";
+            await startServer(resolve(vaultPath));
+            break;
+        }
+        default:
+            console.log(`obsidian-zk — Obsidian Zettelkasten MCP Server
+
+Usage:
+  obsidian-zk init              Interactive setup wizard
+  obsidian-zk update            Sync templates & run migrations
+  obsidian-zk serve --vault .   Start MCP server (called by Claude Code)
+
+Options:
+  --vault PATH          Vault path (default: current directory)
+`);
+            process.exit(command ? 1 : 0);
+    }
+}
+main().catch((err) => {
+    console.error(err);
+    process.exit(1);
+});
+//# sourceMappingURL=index.js.map

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package/dist/db/index.d.ts

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+/**
+ * Database connection + indexing.
+ */
+import Database from "better-sqlite3";
+export declare class ZkDatabase {
+    db: Database.Database;
+    vaultRoot: string;
+    constructor(vaultRoot: string);
+    reindex(): {
+        added: number;
+        updated: number;
+        removed: number;
+    };
+    getNoteByPath(relPath: string): any;
+    getNoteById(zkId: string): any;
+    getNotesByType(type: string): any[];
+    getNotesByStatus(status: string): any[];
+    getNotesByFolder(folder: string): any[];
+    listNotes(filters: {
+        type?: string;
+        status?: string;
+        folder?: string;
+    }): any[];
+    getAllZkIds(): Map<string, {
+        path: string;
+        title: string;
+    }>;
+    getUnprocessed(type?: string): any[];
+    getOrphans(folder?: string): any[];
+    getLinksFrom(relPath: string): any[];
+    getLinksTo(title: string): any[];
+    findConnections(notePath: string): {
+        path: string;
+        title: string;
+        score: number;
+        reasons: string[];
+        summary: string;
+        type: string;
+    }[];
+    getStats(): {
+        total: any;
+        byType: any[];
+        byStatus: any[];
+        linkCount: any;
+        lastIndex: any;
+    };
+    close(): void;
+}
+//# sourceMappingURL=index.d.ts.map

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package/dist/db/index.js

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+/**
+ * Database connection + indexing.
+ */
+import Database from "better-sqlite3";
+import { createHash } from "node:crypto";
+import { readFileSync, existsSync, mkdirSync } from "node:fs";
+import { join, dirname, basename } from "node:path";
+import { CREATE_TABLES, SCHEMA_VERSION } from "./schema.js";
+import { scanVault } from "../vault/scanner.js";
+import { parseFrontmatter, getBody, getTags, getWikilinks } from "../vault/parser.js";
+export class ZkDatabase {
+    db;
+    vaultRoot;
+    constructor(vaultRoot) {
+        this.vaultRoot = vaultRoot;
+        const dbDir = join(vaultRoot, ".zk");
+        if (!existsSync(dbDir))
+            mkdirSync(dbDir, { recursive: true });
+        const dbPath = join(dbDir, "zettelkasten.db");
+        this.db = new Database(dbPath);
+        this.db.pragma("journal_mode = WAL");
+        this.db.exec(CREATE_TABLES);
+        this.db.prepare("INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)").run("schema_version", String(SCHEMA_VERSION));
+    }
+    reindex() {
+        const notes = scanVault(this.vaultRoot);
+        const currentPaths = new Set(notes.map((n) => n.relPath));
+        let added = 0, updated = 0, removed = 0;
+        // Remove deleted notes
+        const dbPaths = this.db.prepare("SELECT path FROM notes").all();
+        const removePaths = dbPaths.filter((r) => !currentPaths.has(r.path));
+        const deleteNote = this.db.prepare("DELETE FROM notes WHERE path = ?");
+        const deleteLinks = this.db.prepare("DELETE FROM links WHERE source = ?");
+        for (const { path } of removePaths) {
+            deleteNote.run(path);
+            deleteLinks.run(path);
+            removed++;
+        }
+        // Upsert notes
+        const getHash = this.db.prepare("SELECT content_hash FROM notes WHERE path = ?");
+        const upsert = this.db.prepare(`
+      INSERT OR REPLACE INTO notes (path, title, zk_id, type, status, folder, tags, summary, created, modified, content_hash)
+      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+    `);
+        const insertLink = this.db.prepare("INSERT OR REPLACE INTO links (source, target, link_type) VALUES (?, ?, ?)");
+        const transaction = this.db.transaction(() => {
+            for (const note of notes) {
+                const fullPath = join(this.vaultRoot, note.relPath);
+                let content;
+                try {
+                    content = readFileSync(fullPath, "utf-8");
+                }
+                catch {
+                    continue;
+                }
+                const hash = createHash("md5").update(content).digest("hex");
+                const existing = getHash.get(note.relPath);
+                if (existing?.content_hash === hash)
+                    continue;
+                const fm = parseFrontmatter(fullPath);
+                const body = getBody(fullPath);
+                const title = basename(note.relPath, ".md");
+                const folder = dirname(note.relPath).split("/")[0] || "";
+                const tags = getTags(fm);
+                const summary = body.trim().slice(0, 200);
+                upsert.run(note.relPath, title, fm.zk_id || null, fm.type || null, fm.status || null, folder, JSON.stringify(tags), summary, fm.date || null, fm.last_modified || null, hash);
+                // Update links
+                deleteLinks.run(note.relPath);
+                const wikilinks = getWikilinks(fullPath);
+                for (const target of wikilinks) {
+                    insertLink.run(note.relPath, target, null);
+                }
+                if (existing)
+                    updated++;
+                else
+                    added++;
+            }
+        });
+        transaction();
+        this.db.prepare("INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)").run("last_index", new Date().toISOString());
+        return { added, updated, removed };
+    }
+    getNoteByPath(relPath) {
+        return this.db.prepare("SELECT * FROM notes WHERE path = ?").get(relPath);
+    }
+    getNoteById(zkId) {
+        return this.db.prepare("SELECT * FROM notes WHERE zk_id = ?").get(zkId);
+    }
+    getNotesByType(type) {
+        return this.db.prepare("SELECT * FROM notes WHERE type = ?").all(type);
+    }
+    getNotesByStatus(status) {
+        return this.db.prepare("SELECT * FROM notes WHERE status = ?").all(status);
+    }
+    getNotesByFolder(folder) {
+        return this.db.prepare("SELECT * FROM notes WHERE folder = ?").all(folder);
+    }
+    listNotes(filters) {
+        let sql = "SELECT * FROM notes WHERE 1=1";
+        const params = [];
+        if (filters.type) {
+            sql += " AND type = ?";
+            params.push(filters.type);
+        }
+        if (filters.status) {
+            sql += " AND status = ?";
+            params.push(filters.status);
+        }
+        if (filters.folder) {
+            sql += " AND folder = ?";
+            params.push(filters.folder);
+        }
+        sql += " ORDER BY path";
+        return this.db.prepare(sql).all(...params);
+    }
+    getAllZkIds() {
+        const rows = this.db.prepare("SELECT zk_id, path, title FROM notes WHERE zk_id IS NOT NULL AND zk_id != ''").all();
+        const map = new Map();
+        for (const r of rows)
+            map.set(r.zk_id, { path: r.path, title: r.title });
+        return map;
+    }
+    getUnprocessed(type) {
+        let sql = "SELECT * FROM notes WHERE status IN ('unprocessed', 'draft')";
+        const params = [];
+        if (type) {
+            sql += " AND type = ?";
+            params.push(type);
+        }
+        sql += " ORDER BY folder, path";
+        return this.db.prepare(sql).all(...params);
+    }
+    getOrphans(folder) {
+        // Notes with no incoming links
+        let sql = `
+      SELECT n.* FROM notes n
+      LEFT JOIN links l ON l.target = n.title
+      WHERE l.target IS NULL
+    `;
+        const params = [];
+        if (folder) {
+            sql += " AND n.folder = ?";
+            params.push(folder);
+        }
+        sql += " ORDER BY n.path";
+        return this.db.prepare(sql).all(...params);
+    }
+    getLinksFrom(relPath) {
+        return this.db.prepare("SELECT * FROM links WHERE source = ?").all(relPath);
+    }
+    getLinksTo(title) {
+        return this.db.prepare("SELECT * FROM links WHERE target = ?").all(title);
+    }
+    findConnections(notePath) {
+        const note = this.getNoteByPath(notePath);
+        if (!note)
+            return [];
+        const noteTags = JSON.parse(note.tags || "[]");
+        const noteTitle = note.title;
+        const existingLinks = new Set(this.getLinksFrom(notePath).map((l) => l.target));
+        const allNotes = this.db.prepare("SELECT * FROM notes WHERE path != ?").all(notePath);
+        const candidates = [];
+        for (const other of allNotes) {
+            if (existingLinks.has(other.title))
+                continue;
+            let score = 0;
+            const reasons = [];
+            // Shared tags
+            const otherTags = JSON.parse(other.tags || "[]");
+            const shared = noteTags.filter((t) => otherTags.includes(t));
+            score += shared.length * 2;
+            reasons.push(...shared.map((t) => `tag:${t}`));
+            // Keyword overlap in summary
+            const noteWords = new Set((note.summary || "").toLowerCase().match(/[а-яієїґa-z]{4,}/g) ?? []);
+            const otherWords = (other.summary || "").toLowerCase().match(/[а-яієїґa-z]{4,}/g) ?? [];
+            const kwMatches = otherWords.filter((w) => noteWords.has(w)).length;
+            score += kwMatches;
+            if (score >= 2) {
+                candidates.push({ path: other.path, title: other.title, score, reasons, summary: other.summary || "", type: other.type || "" });
+            }
+        }
+        return candidates.sort((a, b) => b.score - a.score).slice(0, 15);
+    }
+    getStats() {
+        const total = this.db.prepare("SELECT COUNT(*) as c FROM notes").get().c;
+        const byType = this.db.prepare("SELECT type, COUNT(*) as c FROM notes GROUP BY type").all();
+        const byStatus = this.db.prepare("SELECT status, COUNT(*) as c FROM notes GROUP BY status").all();
+        const linkCount = this.db.prepare("SELECT COUNT(*) as c FROM links").get().c;
+        const lastIndex = this.db.prepare("SELECT value FROM meta WHERE key = 'last_index'").get()?.value;
+        return { total, byType, byStatus, linkCount, lastIndex };
+    }
+    close() {
+        this.db.close();
+    }
+}
+//# sourceMappingURL=index.js.map

package/dist/db/index.js.map

@@ -0,0 +1 @@
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package/dist/db/schema.d.ts

@@ -0,0 +1,6 @@
+/**
+ * SQLite schema + migrations.
+ */
+export declare const SCHEMA_VERSION = 1;
+export declare const CREATE_TABLES = "\nCREATE TABLE IF NOT EXISTS notes (\n  path TEXT PRIMARY KEY,\n  title TEXT,\n  zk_id TEXT,\n  type TEXT,\n  status TEXT,\n  folder TEXT,\n  tags TEXT,\n  summary TEXT,\n  created TEXT,\n  modified TEXT,\n  content_hash TEXT\n);\n\nCREATE TABLE IF NOT EXISTS links (\n  source TEXT NOT NULL,\n  target TEXT NOT NULL,\n  link_type TEXT,\n  PRIMARY KEY (source, target)\n);\n\nCREATE TABLE IF NOT EXISTS meta (\n  key TEXT PRIMARY KEY,\n  value TEXT\n);\n\nCREATE INDEX IF NOT EXISTS idx_notes_type ON notes(type);\nCREATE INDEX IF NOT EXISTS idx_notes_status ON notes(status);\nCREATE INDEX IF NOT EXISTS idx_notes_zk_id ON notes(zk_id);\nCREATE INDEX IF NOT EXISTS idx_links_target ON links(target);\n";
+//# sourceMappingURL=schema.d.ts.map

package/dist/db/schema.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../src/db/schema.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,eAAO,MAAM,cAAc,IAAI,CAAC;AAEhC,eAAO,MAAM,aAAa,msBA+BzB,CAAC"}

package/dist/db/schema.js

@@ -0,0 +1,37 @@
+/**
+ * SQLite schema + migrations.
+ */
+export const SCHEMA_VERSION = 1;
+export const CREATE_TABLES = `
+CREATE TABLE IF NOT EXISTS notes (
+  path TEXT PRIMARY KEY,
+  title TEXT,
+  zk_id TEXT,
+  type TEXT,
+  status TEXT,
+  folder TEXT,
+  tags TEXT,
+  summary TEXT,
+  created TEXT,
+  modified TEXT,
+  content_hash TEXT
+);
+
+CREATE TABLE IF NOT EXISTS links (
+  source TEXT NOT NULL,
+  target TEXT NOT NULL,
+  link_type TEXT,
+  PRIMARY KEY (source, target)
+);
+
+CREATE TABLE IF NOT EXISTS meta (
+  key TEXT PRIMARY KEY,
+  value TEXT
+);
+
+CREATE INDEX IF NOT EXISTS idx_notes_type ON notes(type);
+CREATE INDEX IF NOT EXISTS idx_notes_status ON notes(status);
+CREATE INDEX IF NOT EXISTS idx_notes_zk_id ON notes(zk_id);
+CREATE INDEX IF NOT EXISTS idx_links_target ON links(target);
+`;
+//# sourceMappingURL=schema.js.map

package/dist/db/schema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"schema.js","sourceRoot":"","sources":["../../src/db/schema.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAC;AAEhC,MAAM,CAAC,MAAM,aAAa,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA+B5B,CAAC"}

package/dist/init/scaffold.d.ts

@@ -0,0 +1,3 @@
+import type { WizardAnswers } from "./wizard.js";
+export declare function scaffold(answers: WizardAnswers): void;
+//# sourceMappingURL=scaffold.d.ts.map

package/dist/init/scaffold.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"scaffold.d.ts","sourceRoot":"","sources":["../../src/init/scaffold.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AA4BjD,wBAAgB,QAAQ,CAAC,OAAO,EAAE,aAAa,QA+F9C"}