# 1. Clone and install
git clone https://github.com/YOUR_USERNAME/obsidian-mcp.git
cd obsidian-mcp
npm install

# If on Node 25+ (no prebuilt better-sqlite3 binary yet), build from source:
npm run rebuild:sqlite

# 2. Build
npm run build

# 3. Copy and edit .env
cp .env.example .env
# Set VAULT_PATH to your Obsidian vault directory

# 4. Run (stdio mode)
VAULT_PATH=/path/to/your/vault npm start

{
  "mcpServers": {
    "obsidian": {
      "command": "node",
      "args": ["/absolute/path/to/obsidian-mcp/dist/index.js"],
      "env": {
        "VAULT_PATH": "/absolute/path/to/your/vault"
      }
    }
  }
}

# On EC2: generate a deploy key (read-only) for the vault repo
ssh-keygen -t ed25519 -C "ec2-vault-deploy" -f ~/.ssh/vault_deploy_key -N ""
cat ~/.ssh/vault_deploy_key.pub
# Add the public key to your vault repo as a read-only deploy key on GitHub

# On EC2 (as ec2-user):
export REPO_URL="https://github.com/YOUR_USERNAME/obsidian-mcp.git"
export VAULT_REPO="git@github.com:YOUR_USERNAME/obsidian-vault.git"
bash scripts/setup-ec2.sh

sudo apt install -y nginx certbot python3-certbot-nginx

# Copy config and replace domain
sudo cp nginx/obsidian-mcp.conf /etc/nginx/sites-available/obsidian-mcp
sudo ln -s /etc/nginx/sites-available/obsidian-mcp /etc/nginx/sites-enabled/
# Edit: sed -i 's/mcp.yourdomain.com/your.actual.domain/g' /etc/nginx/sites-available/obsidian-mcp

sudo certbot --nginx -d your.actual.domain
sudo systemctl reload nginx

# Edit VAULT_DIR in the plist first
nano launchd/com.obsidian.sync.plist

# Install
cp launchd/com.obsidian.sync.plist ~/Library/LaunchAgents/
launchctl load ~/Library/LaunchAgents/com.obsidian.sync.plist

# Verify
launchctl list | grep obsidian
tail -f /tmp/obsidian-sync.log

{
  "mcpServers": {
    "obsidian-remote": {
      "url": "https://your.actual.domain/sse",
      "headers": {
        "Authorization": "Bearer YOUR_MCP_AUTH_TOKEN"
      }
    }
  }
}

User: "Quiz me on machine learning"
  → cross_question(topic="machine learning", depth="medium")
  ← Server returns: relevant notes + due questions

Claude reads notes, asks due questions first, then generates new ones
  → submit_review(question_id=42, grade="good")
  ← SM-2 schedules next review in N days

  → add_questions(note_path="ML/Backprop.md", questions=[...])
  ← Stored for future review sessions

User: "How am I doing on ML?"
  → get_topic_mastery(topic="machine learning")
  ← Stats: 23 questions, 18 reviewed, avg ease 2.3, 3 weak areas

obsidian-mcp/
├── src/
│   ├── index.ts              # Entry point (stdio / HTTP)
│   ├── server.ts             # McpServer factory
│   ├── db/
│   │   ├── schema.ts         # SQLite init (FTS5, embeddings, SM-2 state)
│   │   └── sm2.ts            # SM-2 algorithm
│   ├── embeddings/
│   │   └── model.ts          # @xenova/transformers wrapper + cosine fallback
│   ├── vault/
│   │   ├── parser.ts         # Markdown → Note (gray-matter, wikilinks, tags)
│   │   ├── indexer.ts        # Full scan + chokidar file watcher
│   │   └── search.ts         # FTS5 + semantic + hybrid + topic search
│   ├── tools/
│   │   ├── vault.ts          # Vault reading tools
│   │   ├── questions.ts      # Question CRUD tools
│   │   └── review.ts         # Active recall + SM-2 tools
│   └── transport/
│       └── http.ts           # Express SSE + bearer auth
├── systemd/                  # EC2 systemd units + timer
├── launchd/                  # Mac launchd plist (auto git push)
├── nginx/                    # nginx reverse proxy config
└── scripts/
    └── setup-ec2.sh          # EC2 one-shot bootstrap

# Test if sqlite-vec loads on your system
node -e "require('sqlite-vec')"

# Manual backup
cp data/obsidian-mcp.db "data/obsidian-mcp-$(date +%Y%m%d).db"

# Cron backup on EC2 (add to crontab)
0 3 * * * sqlite3 /home/ec2-user/obsidian-mcp/data/obsidian-mcp.db ".backup '/home/ec2-user/backups/obsidian-mcp-$(date +\%Y\%m\%d).db'"