beads/docs/SETUP.md

Setup Command Reference

For: Setting up beads integration with AI coding tools Version: 0.29.0+

Overview

The bd setup command configures beads integration with AI coding tools. It supports five integrations:

Tool	Command	Integration Type
Factory.ai (Droid)	bd setup factory	AGENTS.md file (universal standard)
Claude Code	bd setup claude	SessionStart/PreCompact hooks
Gemini CLI	bd setup gemini	SessionStart/PreCompress hooks
Cursor IDE	bd setup cursor	Rules file (.cursor/rules/beads.mdc)
Aider	bd setup aider	Config file (.aider.conf.yml)

Quick Start

# Install integration for your tool
bd setup factory   # For Factory.ai Droid (and other AGENTS.md-compatible tools)
bd setup claude    # For Claude Code
bd setup gemini    # For Gemini CLI
bd setup cursor    # For Cursor IDE
bd setup aider     # For Aider

# Verify installation
bd setup factory --check
bd setup claude --check
bd setup gemini --check
bd setup cursor --check
bd setup aider --check

Factory.ai (Droid)

Factory.ai Droid integration uses the AGENTS.md standard, which is compatible with multiple AI coding assistants.

Installation

# Create or update AGENTS.md with beads integration
bd setup factory

What Gets Installed

Creates or updates AGENTS.md in your project root with:

• Issue tracking workflow instructions
• Quick command reference
• Issue types and priorities
• Auto-sync explanation
• Important rules for AI agents

The beads section is wrapped in HTML comments (<!-- BEGIN/END BEADS INTEGRATION -->) for safe updates.

AGENTS.md Standard

AGENTS.md is an industry-standard format for AI coding agent instructions, supported by:

• Factory.ai Droid - Specialized coding agents
• Cursor - Also reads AGENTS.md (in addition to .cursor/rules)
• Aider - Can be configured to read AGENTS.md
• Gemini CLI - Google's command-line AI assistant
• Jules - Google's coding assistant
• Codex - OpenAI's code generation model
• Zed - AI-enhanced editor
• And many more emerging tools

Using AGENTS.md means one configuration file works across your entire AI tool ecosystem.

Flags

Flag	Description
--check	Check if beads section exists in AGENTS.md
--remove	Remove beads section from AGENTS.md

Examples

# Check if beads section is in AGENTS.md
bd setup factory --check
# Output: ✓ Factory.ai integration installed: AGENTS.md
#         Beads section found in AGENTS.md

# Remove beads section
bd setup factory --remove

How It Works

Factory Droid and other AGENTS.md-compatible tools automatically read AGENTS.md from:

1. Current working directory (./AGENTS.md)
2. Parent directories up to repo root
3. Personal override (~/.factory/AGENTS.md)

The beads section teaches AI agents:

• To use bd ready for finding work
• To use bd create for tracking new issues
• To use bd sync at session end
• The complete workflow pattern and best practices

Updating Existing AGENTS.md

If you already have an AGENTS.md file with other project instructions:

• bd setup factory will append the beads section
• Re-running it will update the existing beads section (idempotent)
• The markers (<!-- BEGIN/END BEADS INTEGRATION -->) ensure safe updates

When to Use This vs Other Integrations

Use Factory integration when:

• ✅ You use Factory.ai Droid
• ✅ You want one config file for multiple AI tools
• ✅ You prefer the AGENTS.md standard
• ✅ Your team uses multiple AI coding assistants

Use other integrations when:

• ✅ You only use Claude Code → bd setup claude (hooks are more dynamic)
• ✅ You need tool-specific features (like Claude's stealth mode)

You can use multiple integrations simultaneously - they complement each other!

Claude Code

Claude Code integration uses hooks to automatically inject beads workflow context at session start and before context compaction.

Installation

# Global installation (recommended)
bd setup claude

# Project-only installation
bd setup claude --project

# With stealth mode (flush only, no git operations)
bd setup claude --stealth

What Gets Installed

Global installation (~/.claude/settings.json):

• SessionStart hook: Runs bd prime when a new session starts
• PreCompact hook: Runs bd prime before context compaction

Project installation (.claude/settings.local.json):

• Same hooks, but only active for this project

Flags

Flag	Description
--check	Check if integration is installed
--remove	Remove beads hooks
--project	Install for this project only (not globally)
--stealth	Use bd prime --stealth (flush only, no git operations)

Examples

# Check if hooks are installed
bd setup claude --check
# Output: ✓ Global hooks installed: /Users/you/.claude/settings.json

# Remove hooks
bd setup claude --remove

# Install project-specific hooks with stealth mode
bd setup claude --project --stealth

How It Works

The hooks call bd prime which:

1. Outputs workflow context for Claude to read
2. Syncs any pending changes
3. Ensures Claude always knows how to use beads

This is more context-efficient than MCP tools (~1-2k tokens vs 10-50k for MCP schemas).

Gemini CLI

Gemini CLI integration uses hooks to automatically inject beads workflow context at session start and before context compression.

Installation

# Global installation (recommended)
bd setup gemini

# Project-only installation
bd setup gemini --project

# With stealth mode (flush only, no git operations)
bd setup gemini --stealth

What Gets Installed

Global installation (~/.gemini/settings.json):

• SessionStart hook: Runs bd prime when a new session starts
• PreCompress hook: Runs bd prime before context compression

Project installation (.gemini/settings.json):

• Same hooks, but only active for this project

Flags

Flag	Description
--check	Check if integration is installed
--remove	Remove beads hooks
--project	Install for this project only (not globally)
--stealth	Use bd prime --stealth (flush only, no git operations)

Examples

# Check if hooks are installed
bd setup gemini --check
# Output: ✓ Global hooks installed: /Users/you/.gemini/settings.json

# Remove hooks
bd setup gemini --remove

# Install project-specific hooks with stealth mode
bd setup gemini --project --stealth

How It Works

The hooks call bd prime which:

1. Outputs workflow context for Gemini to read
2. Syncs any pending changes
3. Ensures Gemini always knows how to use beads

This works identically to Claude Code integration, using Gemini CLI's hook system (SessionStart and PreCompress events).

Cursor IDE

Cursor integration creates a rules file that provides beads workflow context to the AI.

Installation

bd setup cursor

What Gets Installed

Creates .cursor/rules/beads.mdc with:

• Core workflow rules (track work in bd, not markdown TODOs)
• Quick command reference
• Workflow pattern (ready → claim → work → close → sync)
• Context loading instructions

Flags

Flag	Description
--check	Check if integration is installed
--remove	Remove beads rules file

Examples

# Check if rules are installed
bd setup cursor --check
# Output: ✓ Cursor integration installed: .cursor/rules/beads.mdc

# Remove rules
bd setup cursor --remove

How It Works

Cursor reads .cursor/rules/*.mdc files and includes them in the AI's context. The beads rules file teaches the AI:

• To use bd ready for finding work
• To use bd create for tracking new issues
• To use bd sync at session end
• The basic workflow pattern

Aider

Aider integration creates configuration files that teach the AI about beads, while respecting Aider's human-in-the-loop design.

Installation

bd setup aider

What Gets Installed

File	Purpose
.aider.conf.yml	Points Aider to read the instructions file
.aider/BEADS.md	Workflow instructions for the AI
.aider/README.md	Quick reference for humans

Flags

Flag	Description
--check	Check if integration is installed
--remove	Remove beads configuration

Examples

# Check if config is installed
bd setup aider --check
# Output: ✓ Aider integration installed: .aider.conf.yml

# Remove configuration
bd setup aider --remove

How It Works

Unlike Claude Code, Aider requires explicit command execution. The AI will suggest bd commands, which the user runs via /run:

You: What issues are ready to work on?

Aider: Let me check. Run:
/run bd ready

You: [runs the command]

Aider: Great! To claim bd-42, run:
/run bd update bd-42 --status in_progress

This respects Aider's philosophy of keeping humans in control while still leveraging beads for issue tracking.

Comparison

Feature	Factory.ai	Claude Code	Gemini CLI	Cursor	Aider
Command execution	Automatic	Automatic	Automatic	Automatic	Manual (/run)
Context injection	AGENTS.md	Hooks	Hooks	Rules file	Config file
Global install	No (per-project)	Yes	Yes	No (per-project)	No (per-project)
Stealth mode	N/A	Yes	Yes	N/A	N/A
Standard format	Yes (AGENTS.md)	No (proprietary)	No (proprietary)	No (proprietary)	No (proprietary)
Multi-tool compatible	Yes	No	No	No	No

Best Practices

1. Start with Factory integration - Creates AGENTS.md which works across multiple AI tools:

   bd setup factory
   

2. Add tool-specific integrations as needed - Claude hooks, Cursor rules, or Aider config for tool-specific features

3. Install globally for Claude Code or Gemini CLI - You'll get beads context in every project automatically

4. Use stealth mode in CI/CD - bd setup claude --stealth or bd setup gemini --stealth avoids git operations that might fail in automated environments

5. Commit AGENTS.md to git - This ensures all team members and AI tools get the same instructions

6. Run bd doctor after setup - Verifies the integration is working:

   bd doctor | grep -iE "claude|gemini"
   # Claude Integration: Hooks installed (CLI mode)
   # Gemini CLI Integration: Hooks installed
   

Troubleshooting

"Hooks not working"

1. Restart your AI tool after installation
2. Verify with bd setup <tool> --check
3. Check bd doctor output for integration status

"Context not appearing"

For Claude Code, ensure bd prime works standalone:

bd prime

If this fails, fix the underlying beads issue first.

"Want to switch from global to project hooks"

# Remove global hooks
bd setup claude --remove

# Install project hooks
bd setup claude --project

Related Documentation

• CLAUDE_INTEGRATION.md - Design decisions for Claude Code integration
• AIDER_INTEGRATION.md - Detailed Aider workflow guide
• QUICKSTART.md - Getting started with beads
• CLI_REFERENCE.md - Full command reference