Brain CLI Expert

You are an expert on the brain CLI - a personal knowledge management tool with hierarchical Markdown files, SQLite storage, and semantic search.

Quick Reference

Command	Description
brain init [path]	Initialize brain directory
brain add "text"	Add timestamped note to today's file
brain add -f file.md "text"	Add to specific file
brain add --ref /path "text"	Add note referencing external file
brain new "path/name"	Create new entry, opens in editor
brain list	Show recent entries
brain list --tree	Show directory structure
brain show <path>	Display entry content
brain edit <path>	Open entry in editor
brain delete <path>	Delete entry (file + database)
brain rm <path>	Alias for delete
brain sync	Sync files to database
brain sync --force	Re-embed everything
brain search "query"	Semantic search (default)
brain search --exact "term"	Full-text search (FTS5)
brain config show	Display configuration
brain todo add "text"	Create a new todo
brain todo list	List open todos
brain todo done <id>	Mark todo as complete
brain todo cancel <id>	Cancel a todo
brain todo edit <id>	Edit todo in editor
brain todo rm <id>	Delete todo permanently
brain cron install	Install auto-sync cron job
brain cron status	Check auto-sync status
brain cron remove	Remove auto-sync cron job

File Structure

Brain organizes files hierarchically:

~/Documents/brain/
├── 2026/
│   └── 01/
│       ├── 22.md          # Daily journal (timestamped entries)
│       └── 23.md
├── projects/
│   ├── acme.md            # Named entries (by topic)
│   └── startup-ideas.md
├── notes/
│   └── meeting-notes.md
└── .brain.db              # SQLite database (gitignored)

Entry Formats

Daily Files (YYYY/MM/DD.md)

Auto-created when using brain add:

[2026-01-23-143022]
First thought of the day

[2026-01-23-153045]
Another thought with more context

Named Files

Created with brain new:

# Project Title

Content organized however you like.
Can include todos: - [ ] Task here

Search

Semantic Search (default)

Uses OpenAI embeddings for meaning-based search:

brain search "database optimization strategies"

Returns results ranked by semantic similarity.

Full-Text Search (--exact)

Uses SQLite FTS5 for literal text matching:

brain search --exact "PostgreSQL"

Sync Required

Before searching, ensure database is synced:

brain sync

The sync process:

1. Scans all .md files
2. Chunks content (by timestamp blocks or headers)
3. Generates embeddings for new/changed chunks
4. Updates FTS5 index

Use brain sync --force to re-embed everything.

Configuration

Config stored at ~/.brain.json:

{
  "path": "/Users/taras/Documents/brain",
  "editor": "code",
  "embeddingModel": "text-embedding-3-small"
}

Manage with:

• brain config show - view config
• brain config set editor vim - update value

Common Workflows

Quick Capture

brain add "Idea: could use SQLite for local caching"

Reference External Code

brain add --ref ./src/api/auth.ts "Need to add rate limiting here"

Find Related Notes

brain search "authentication patterns"

Create Project Notes

brain new "projects/new-feature"
# Opens editor with # New Feature header

Delete Entries

brain delete 2026/01/22           # Delete with confirmation
brain rm notes/old-project        # Alias, same behavior
brain rm --force notes/temp       # Skip confirmation
brain rm --db-only notes/draft    # Keep file, remove from database

Todo Management

# Add todos with options
brain todo add "Review PR"
brain todo add -p myproject "Ship feature"
brain todo add -d tomorrow "Deploy to prod"
brain todo add -p work -d "next week" "Plan sprint"

# List and filter
brain todo list                    # Open todos
brain todo list --all              # Include done/cancelled
brain todo list -p myproject       # Filter by project

# Complete and manage
brain todo done 1 2 3              # Mark multiple as done
brain todo cancel 1                # Cancel a todo
brain todo edit 1                  # Edit in $EDITOR
brain todo rm 1                    # Delete permanently

Automatic Sync

# Set up background sync (runs every N minutes)
brain cron install                 # Default: 5 minutes
brain cron install --interval 15   # Custom interval

# Check and manage
brain cron status                  # "Active (every 5 minutes)"
brain cron remove                  # Stop auto-sync

Environment

• OPENAI_API_KEY: Required for semantic search embeddings
• EDITOR: Fallback if config.editor not set

Troubleshooting

Issue	Solution
Search returns nothing	Run brain sync first
Embedding errors	Check OPENAI_API_KEY is set
Command not found	Run bun link in brain directory
Wrong brain path	Check brain config show