Obsidian + Claude System

A complete system for managing Obsidian vaults with Claude Code and Cowork. Designed for two vaults (work and personal) with consistent structure, frontmatter schemas, agent skills, automation hooks, and migration tooling.

What’s Included

obsidian-claude-system/
├── skills/
│   └── obsidian-vault-manager/
│       ├── SKILL.md                          # Claude Code skill definition
│       ├── references/
│       │   ├── frontmatter-schemas.md        # Complete YAML schema for all note types
│       │   └── templates.md                  # Note body templates
│       └── scripts/
│           ├── vault-health-check.sh         # Vault health audit script
│           └── process-inbox.py              # Auto-sort inbox notes
├── hooks/
│   ├── hook-configs.json                     # Claude Code hook configuration (incl. QMD Stop hook)
│   ├── update-modified.py                    # Auto-update modified timestamps
│   ├── link-to-daily.py                      # Auto-link new notes to daily note
│   └── validate-frontmatter.py              # Frontmatter validation
├── templates/
│   ├── work/CLAUDE.md                        # Agent instructions for work vault
│   └── personal/CLAUDE.md                    # Agent instructions for personal vault
├── scripts/
│   └── setup-vault.sh                        # Vault bootstrapping script
├── docs/
│   ├── vault-migration-guide.md              # How to convert an existing vault
│   └── plugin-guide.md                       # Recommended Obsidian plugins
└── README.md                                 # This file

Quick Start

1. Install Kepano’s Official Obsidian Skills Plugin

This is the foundation — it teaches Claude the correct Obsidian file formats (markdown syntax, wikilinks, callouts, Bases, JSON Canvas, and the Obsidian CLI). Install it first:

# From the Claude Code plugin marketplace
/plugin marketplace add kepano/obsidian-skills
/plugin install obsidian@obsidian-skills

Or install manually by cloning into your vault’s .claude/ folder:

cd ~/obsidian-vaults/work
git clone https://github.com/kepano/obsidian-skills.git .claude/skills/obsidian-skills

This gives Claude 5 skills: obsidian-markdown (wikilinks, embeds, callouts, properties), obsidian-bases (database views, filters, formulas), json-canvas (whiteboards), obsidian-cli (read/create/search notes via CLI), and defuddle (clean web clipping).

2. Install the Vault Manager Skill (this package)

This skill layers on top of Kepano’s — it adds vault structure, workflows, frontmatter schemas, and lifecycle management. Copy it into your Claude Code skills directory:

cp -r skills/obsidian-vault-manager ~/.claude/skills/

Or if using Cowork, place it in your mounted .skills/skills/ directory.

How the two skills work together: Kepano’s skills handle the format layer (how to write correct Obsidian markdown, how to use the CLI, how to structure a .base file). The vault manager handles the workflow layer (where notes go, what frontmatter to use, how to do daily reviews, when to archive, how to process the inbox).

3. Install QMD (Local Semantic Search)

QMD by Tobi Lütke is a local search engine that indexes your vault for semantic search. It combines BM25 keyword matching, vector search, and LLM reranking — all on-device.

# Install globally
npm install -g @tobilu/qmd
# or
bun install -g @tobilu/qmd

Set up a collection for each vault:

qmd collection add ~/obsidian-vaults/work --name work
qmd context add work "Work vault: projects, meetings, decisions, standups, people, ideas, resources"

qmd collection add ~/obsidian-vaults/personal --name personal
qmd context add personal "Personal vault: journal, health, finance, learning, ideas, lists, people"

# Build initial index
qmd embed

The Stop hook in hooks/hook-configs.json automatically runs qmd embed after every Claude response, so the index stays fresh without blocking individual edits.

4. Set up new vaults

# Work vault
./scripts/setup-vault.sh ~/obsidian-vaults/work work

# Personal vault
./scripts/setup-vault.sh ~/obsidian-vaults/personal personal

5. Configure hooks

Add the hooks from hooks/hook-configs.json to your Claude Code settings:

# Edit your Claude Code settings
claude config edit
# OR
vim ~/.claude/settings.json

Merge the hooks object from hook-configs.json into your settings. This includes the Stop hook that runs qmd embed after each agent turn.

6. Install Obsidian plugins

Open each vault in Obsidian and install the recommended plugins from docs/plugin-guide.md. At minimum: Dataview, Templater, and Calendar.

7. Migrate existing notes (if applicable)

Follow the step-by-step process in docs/vault-migration-guide.md. Ask Claude Code to help:

"Help me migrate my existing Obsidian vault at ~/Documents/notes to the new format. It's my work vault."

How It Works

The Skill

The obsidian-vault-manager skill teaches Claude Code how to work with your vaults. It understands the folder structure, frontmatter schemas, naming conventions, and linking patterns. When you say things like “take meeting notes” or “what’s on my plate,” the skill kicks in.

QMD Search

QMD indexes your vaults locally for semantic search. When you ask “what did I write about that architecture discussion last month,” QMD finds the right notes even if your phrasing doesn’t match the exact words. The Stop hook runs qmd embed once after each Claude response — so the index stays current without slowing down individual edits.

The Hooks

Hooks automate housekeeping:

• QMD re-index (Stop): Runs qmd embed after each agent turn to keep the search index fresh
• Modified timestamp (PostToolUse): Auto-updates when you edit a note through Claude
• Daily note linking (PostToolUse): New notes automatically get linked from today’s daily note
• Frontmatter validation: Catches schema violations before they accumulate

The CLAUDE.md

Each vault has a CLAUDE.md at its root. This is the first thing Claude reads when it opens the vault. It contains vault-specific instructions, common tasks, and tag taxonomies.

Two Vaults, One System

Work and personal vaults share the same structure and conventions but have different folder additions and different CLAUDE.md instructions. The skill handles both — it determines which vault to use based on context.

Customization

This system is designed as a starting point. Customize it:

• Add note types: Define new frontmatter schemas in references/frontmatter-schemas.md
• Add tags: Update the tag taxonomies in each vault’s CLAUDE.md
• Add areas: Create new subfolders under 03-areas/ for your specific responsibilities
• Modify templates: Edit references/templates.md and copy to _templates/
• Add hooks: Extend hook-configs.json with your own automation

Note Types at a Glance