Obsidian PKM Plugin

Give Claude persistent, structured memory across conversations using your Obsidian vault. Read, write, search, and navigate your knowledge base — all from within Claude Code.

Under the hood, this Claude Code plugin provides 20 MCP tools for note creation, semantic search, graph traversal, metadata queries, and session memory — plus agents, hooks, and skills for seamless workflow integration. Published on npm as obsidian-pkm.

Why

Claude Code has built-in memory, but it's flat text files scoped to individual projects — no structure, no search beyond exact matches, no connections between notes, and no way to query across projects. As knowledge grows, it doesn't scale. This server replaces that with a proper PKM layer: structured notes with enforced metadata, semantic search, a navigable knowledge graph, and cross-project access through a single Obsidian vault.

• Structured session memory — Every tool call is logged with timestamps and session IDs, so Claude can recall exactly what was read, written, and searched in previous conversations — not just what was saved to a text file.
• Structured knowledge creation — ADRs, research notes, devlogs, and tasks are created from enforced templates with validated frontmatter — not freeform text dumps. Your vault stays consistent and queryable.
• Semantic discovery — "Find my notes about caching strategies" works even if you never used the word "caching." Conceptual search surfaces relevant knowledge that keyword search misses.
• Graph-aware connections — Claude explores your knowledge graph by following wikilinks, discovering related notes by proximity rather than just content. Link suggestions help weave new notes into your existing web of knowledge.
• Knowledge capture — Decisions, tasks, and research findings are captured by specialized agents in the background without interrupting your coding flow.

Without this, knowledge stays fragmented across per-project memory files and chat logs. With it, your AI assistant maintains a unified knowledge base that compounds over time.

https://github.com/user-attachments/assets/58ad9c9b-d987-4728-89e7-33de20b73a38

Features

Knowledge Creation & Editing

Tool	Description
vault_write	Create notes from templates with enforced frontmatter (ADRs, research, devlogs, tasks, etc.)
vault_append	Add content to notes, with positional insert (after/before heading, end of section)
vault_edit	Surgical string replacement for precise edits
vault_update_frontmatter	Atomic YAML frontmatter updates (set, create, remove fields; validates enums by note type)

Discovery & Search

Tool	Description
vault_search	Full-text keyword search across markdown files
vault_semantic_search	Conceptual similarity search via OpenAI embeddings — finds related notes even with different wording
vault_query	Query by YAML frontmatter (type, status, tags, dates, custom fields) with sorting
vault_tags	Discover all tags with per-note counts; folder scoping, glob filters, inline tag parsing
vault_suggest_links	Suggest relevant notes to link based on content similarity

Graph & Connections

Tool	Description
vault_links	Wikilink analysis (incoming and outgoing links for a note)
vault_neighborhood	Graph exploration via BFS wikilink traversal — discover related notes by proximity
vault_add_links	Add annotated wikilinks to a note's section with deduplication
vault_link_health	Audit link quality — find orphans, broken links, weak connections, ambiguous links

Reading & Navigation

Tool	Description
vault_read	Read note contents (pagination by heading, tail, chunk, line range; auto-redirects large files)
vault_peek	Inspect file metadata and structure without reading full content
vault_list	List files and folders
vault_recent	Recently modified files

Organization & Maintenance

Tool	Description
vault_move	Move/rename files with automatic wikilink updating across the vault
vault_trash	Soft-delete to .trash/ (Obsidian convention), warns about broken incoming links

Session Memory

Tool	Description
vault_activity	Cross-conversation memory — logs every tool call with timestamps and session IDs

Agents

4 specialized agents are available via /agents: vault-explorer (research existing knowledge before creating notes), devlog-updater (update devlog after significant work blocks), knowledge-sweeper (capture decisions, research, and tasks after notable sessions), and link-auditor (audit vault link health after bulk note changes). Agents can be @-mentioned and run in foreground or background.

Prerequisites

• Node.js >= 20 (Node 18 is EOL; uses native fetch and ES modules)
• An MCP-compatible client such as Claude Code
• C++ build tools for better-sqlite3 native addon:
  • macOS: xcode-select --install
  • Linux: sudo apt install build-essential python3 (Debian/Ubuntu) or equivalent
  • Windows: Install Visual Studio Build Tools with the "Desktop development with C++" workload

Quick Start

1. Install the Plugin

claude plugin marketplace add AdrianV101/obsidian-pkm-plugin
claude plugin install obsidian-pkm

2. Configure

Run the setup skill in Claude Code:

/obsidian-pkm:setup

The setup skill walks you through vault path, API keys, tool permissions, and verification. Hooks are registered automatically by the plugin system.

Important: Restart your Claude Code session after setup completes so the MCP server picks up the new configuration.

3. Scaffold Your Vault (optional)

If you need templates and the PARA folder structure:

npx obsidian-pkm init

This sets up your vault's directory structure (PARA folders, note templates). Nothing is written until you confirm each step.

Scaffold details

Step 1 — Vault path. Point to an existing Obsidian vault or create a new one. The wizard resolves ~, $HOME, and relative paths automatically. Safety checks prevent using system directories (/, /home, etc.) as a vault. For existing non-empty directories you can use it as-is, create a subfolder inside it, or wipe it (with triple confirmation). You'll be offered an optional backup before any changes.

Step 2 — Note templates. Copies template files into <vault>/05-Templates/. Three options:

• Full set — all 13 templates (adr, daily-note, devlog, fleeting-note, literature-note, meeting-notes, moc, note, permanent-note, project-index, research-note, task, troubleshooting-log)
• Minimal — just note.md (a single generic template)
• Skip — for users with their own templates

Existing templates are never overwritten.

Step 3 — PARA folder structure. Creates 7 top-level folders with _index.md stubs:

Folder	Purpose
00-Inbox/	Quick captures and unsorted notes
01-Projects/	Active project folders
02-Areas/	Ongoing areas of responsibility
03-Resources/	Reference material and reusable knowledge
04-Archive/	Completed or inactive items
05-Templates/	Note templates
06-System/	System configuration and metadata

Each _index.md has type: moc frontmatter. Existing folders and index files are skipped.

4. Verify It Works

Open Claude Code and try:

List the folders in my vault

Claude should call vault_list and show your vault's directory structure. If it works, the server is connected and ready.

5. Enable Semantic Search (optional)

Add your OpenAI API key to ~/.claude/settings.json under the env block:

{
  "env": {
    "VAULT_PATH": "/path/to/vault",
    "OBSIDIAN_PKM_OPENAI_KEY": "sk-your-key-here"
  }
}

Use OBSIDIAN_PKM_OPENAI_KEY (preferred) to avoid conflicts with project-level OpenAI keys. OPENAI_API_KEY is also accepted as a fallback. Restart Claude Code after saving.

This enables vault_semantic_search and vault_suggest_links. Uses text-embedding-3-large with a SQLite + sqlite-vec index stored at .obsidian/semantic-index.db. The index rebuilds automatically — delete the DB file to force a full re-embed.

Vault Structure

The server works with any Obsidian vault. The included templates assume this layout:

Vault/
├── 00-Inbox/
├── 01-Projects/
│   └── ProjectName/
│       ├── _index.md
│       ├── planning/
│       ├── research/
│       └── development/decisions/
├── 02-Areas/
├── 03-Resources/
├── 04-Archive/
├── 05-Templates/          # Note templates loaded by vault_write
└── 06-System/

Templates

vault_write loads all .md files from 05-Templates/ at startup and enforces frontmatter on every note created. Run npx obsidian-pkm init to install them automatically, or copy the files from templates/ manually.

13 included templates: adr, daily-note, devlog, fleeting-note, literature-note, meeting-notes, moc, note, permanent-note, project-index, research-note, task, troubleshooting-log. Add your own templates to 05-Templates/ and they become available to vault_write automatically.

CLAUDE.md for Your Projects

sample-project/CLAUDE.md is a template you can drop into any code repository to wire up Claude Code with your vault. It defines context loading, documentation rules, and ADR/devlog conventions.

Architecture

Module dependencies:

graph LR
    CC[Claude Code] -->|MCP protocol| IDX[index.js]
    IDX --> HND[handlers.js]
    IDX --> E[embeddings.js]
    IDX --> A[activity.js]
    HND --> H[helpers.js]
    HND --> G[graph.js]
    HND --> U[utils.js]
    HND -->|read/write| V[(Obsidian Vault)]
    E -->|embeddings API| OAI[OpenAI]
    E -->|vector store| DB[(SQLite + sqlite-vec)]
    A -->|activity log| DB2[(SQLite)]

File layout:

├── index.js          # MCP server setup, tool registration, lifecycle
├── handlers.js       # Tool handler implementations
├── helpers.js        # Pure functions (path security, filtering, templates, frontmatter)
├── graph.js          # Wikilink resolution and BFS graph traversal
├── embeddings.js     # Semantic index (OpenAI embeddings, SQLite + sqlite-vec)
├── activity.js       # Activity log (session tracking, SQLite)
├── utils.js          # Shared utilities (frontmatter parsing, file listing)
├── cli.js            # CLI entry point (routes `init` subcommand or starts server)
├── init.js           # Vault scaffolding wizard (templates, PARA folders)
├── .claude-plugin/   # Plugin packaging
│   ├── plugin.json   # Plugin manifest (identity, components, permissions)
│   └── marketplace.json  # Self-hosted marketplace entry
├── hooks/            # Claude Code hooks (context loading, project resolution, session start)
├── agents/           # Specialized agents (vault-explorer, devlog-updater, knowledge-sweeper, link-auditor)
├── skills/           # PKM workflow skills (pkm-write, pkm-explore, pkm-session-end)
├── commands/         # Slash commands (setup, init-project)
├── templates/        # Obsidian note templates
├── tests/            # Test suite (Node.js built-in test runner)
├── sample-project/   # Sample CLAUDE.md for your repos
└── docs/             # Supplementary documentation

index.js initializes the semantic index and activity log, then injects them into createHandlers(). All paths passed to tools are relative to vault root. The server includes path security to prevent directory traversal.

How It Works

Knowledge creation is template-based. vault_write loads templates from 05-Templates/, substitutes Templater-compatible variables (<% tp.date.now("YYYY-MM-DD") %>, <% tp.file.title %>), and validates required frontmatter fields (type, created, tags). This ensures every note in your vault has consistent metadata — making it queryable, sortable, and discoverable from day one. Task notes enforce enum validation on status and priority; other types accept project, deciders, due, and source.

Knowledge discovery works at two levels. Keyword search (vault_search) finds exact terms. Semantic search embeds notes using OpenAI and finds conceptually related content — so "managing overwhelm" surfaces notes about "cognitive load" even if those exact words never appear together. The semantic index watches for file changes in real-time and syncs across machines via Obsidian Sync.

Knowledge connections are maintained through Obsidian's [[wikilink]] graph. vault_neighborhood traverses links via BFS to discover related notes by proximity, while vault_suggest_links recommends connections you haven't made yet. vault_move rewrites wikilinks across the vault when you reorganize, and vault_trash warns about links that would break.

Session memory records every tool call with timestamps and session IDs, so Claude can recall what was read, written, or searched in previous conversations. This turns ephemeral chat sessions into a continuous thread of work.

Knowledge capture uses the knowledge-sweeper agent to identify and persist PKM-worthy content from a session (decisions, research findings, tasks, bug root causes). Delegate to it after significant work blocks. The devlog-updater agent handles devlog entries. Both run in the background without interrupting the coding flow.

Fuzzy path resolution lets read-only tools accept short names instead of full vault paths. vault_read({ path: "devlog" }) resolves to 01-Projects/MyApp/development/devlog.md automatically (.md extension optional). Folder-scoped tools like vault_search and vault_query accept partial folder names — folder: "MyApp" resolves to 01-Projects/MyApp. Ambiguous matches return an error listing candidates. Write/destructive tools always require exact paths.

Troubleshooting

better-sqlite3 build fails during install
You need C++ build tools. See Prerequisites for your platform. On Linux, sudo apt install build-essential python3 usually fixes it.

Server starts but all tool calls fail with ENOENT
Your VAULT_PATH is wrong or missing. The server validates this at startup and exits with a clear error. Run /obsidian-pkm:setup to reconfigure the vault path.

vault_write says "no templates available"
Run npx obsidian-pkm init to install templates, or copy the templates/ files from this repo into your vault's 05-Templates/ directory. The server loads templates from there at startup.

Semantic search not appearing in tool list
Set OBSIDIAN_PKM_OPENAI_KEY in ~/.claude/settings.json. See Enable Semantic Search. Without it, vault_semantic_search and vault_suggest_links are hidden entirely.

Server not showing up in Claude Code after install
Run claude mcp list to check. If obsidian-pkm is missing, reinstall the plugin: claude plugin install obsidian-pkm. Then run /obsidian-pkm:setup to configure it.

Semantic index not updating after file changes
Check your Node version with node -v. The file watcher uses fs.watch({ recursive: true }) which requires Node.js >= 20.

Contributing

Contributions are welcome! Please read CONTRIBUTING.md for development setup, code style guidelines, and the pull request process before submitting changes.

See CHANGELOG.md for release history and SECURITY.md to report vulnerabilities.

License

MIT