Setup Command Reference

Last reviewed: 2026-05-08

Freshness source: cmd/bd/setup*.go and internal/recipes/.

For: Setting up beads integration with AI coding tools Version: current CLI behaviour; verify recipe lists against the freshness source above.

Overview

The bd setup command uses a recipe-based architecture to configure beads integration with AI coding tools. Recipes define where workflow instructions are written—built-in recipes handle popular tools, and you can add custom recipes for any tool.

`bd prime` as SSOT

bd prime is the single source of truth for operational workflow commands. The beads section in each tool's instruction file provides a pointer to bd prime for hook-enabled agents (Claude, Gemini) or the full command reference for AGENTS-first agents (Factory, Mux). Codex uses a Beads skill plus generated AGENTS.md guidance that points Codex at that skill.

Profiles

Each integration uses one of two profiles that control how much content is written to tool instruction files (AGENTS.md, CLAUDE.md, or GEMINI.md):

Profile	Used By	Content
`full`	Factory, Mux, OpenCode	Complete command reference, issue types, priorities, workflow
`minimal`	Claude Code, Gemini CLI	Pointer to `bd prime`, quick reference only (~60% smaller)

Hook-enabled agents (Claude, Gemini) use the minimal profile because bd prime injects full context at session start. AGENTS-first agents use the full profile because their instruction file remains the primary integration surface. Skill-aware agents use .agents/skills/beads/SKILL.md, with project AGENTS.md or global $CODEX_HOME/AGENTS.md/~/.codex/AGENTS.md telling Codex when to use the skill.

Profile precedence: If a file already has a full profile section and a minimal profile tool installs to the same file (e.g., via symlinks), the full profile is preserved to avoid information loss.

Built-in Recipes

Recipe	Path	Integration Type
`cursor`	`.cursor/rules/beads.mdc`	Rules file
`windsurf`	`.windsurf/rules/beads.md`	Rules file
`cody`	`.cody/rules/beads.md`	Rules file
`kilocode`	`.kilocode/rules/beads.md`	Rules file
`claude`	`~/.claude/settings.json` + `CLAUDE.md`	SessionStart hook + minimal section
`gemini`	`~/.gemini/settings.json` + `GEMINI.md`	SessionStart hook + minimal section
`factory`	`AGENTS.md`	Marked section
`codex`	`.agents/skills/beads/SKILL.md` + `AGENTS.md`	Beads agent skill + generated skill guidance
`mux`	`AGENTS.md`	Marked section
`aider`	`.aider.conf.yml` + `.aider/`	Multi-file config

Quick Start

# List all available recipes
bd setup --list

# Install integration for your tool
bd setup cursor     # Cursor IDE
bd setup windsurf   # Windsurf
bd setup kilocode   # Kilo Code
bd setup claude     # Claude Code
bd setup gemini     # Gemini CLI
bd setup factory    # Factory.ai Droid
bd setup codex      # Beads agent skill + AGENTS.md guidance
bd setup mux        # Mux
bd setup aider      # Aider

# Verify installation
bd setup cursor --check
bd setup claude --check

# Print template to stdout (for inspection)
bd setup --print

# Write template to custom path
bd setup -o .my-editor/rules.md

# Add a custom recipe
bd setup --add myeditor .myeditor/rules.md
bd setup myeditor  # Now you can use it

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 () with metadata for safe updates. The begin marker includes profile and hash metadata (e.g., ) for freshness detection. Legacy markers without metadata are auto-upgraded on the next install or update.

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 and is current (reports `missing`, `stale`, or `current`)
`--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:

Current working directory (./AGENTS.md)
Parent directories up to repo root
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 dolt push 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 () 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!

Codex CLI

Codex reads project instructions from AGENTS.md in the current working directory or project root, and global instructions from $CODEX_HOME/AGENTS.md when CODEX_HOME is set, otherwise ~/.codex/AGENTS.md. The Codex setup path installs the generic beads agent skill and writes a managed section to the Codex-readable instruction file telling Codex to use that skill for Beads workflow guidance.

Installation

bd setup codex          # Project Beads skill + AGENTS.md guidance
bd setup codex --global # Global Beads skill + global AGENTS.md guidance

What Gets Installed

Project install (bd setup codex):

Creates or updates .agents/skills/beads/SKILL.md
Creates or updates .agents/skills/beads/agents/openai.yaml
Creates or updates project AGENTS.md with a marked section generated by bd setup codex

Global install (bd setup codex --global):

Creates or updates ~/.agents/skills/beads/SKILL.md
Creates or updates ~/.agents/skills/beads/agents/openai.yaml
Creates or updates $CODEX_HOME/AGENTS.md when CODEX_HOME is set, otherwise ~/.codex/AGENTS.md, with a marked section generated by bd setup codex --global

Flags

Flag	Description
`--check`	Check the Beads agent skill and managed Codex `AGENTS.md` guidance
`--remove`	Remove the Beads agent skill and managed Codex `AGENTS.md` guidance
`--global`	Install/check/remove the global skill and global Codex `AGENTS.md` guidance

Notes

Restart Codex if it's already running to pick up the new instructions.
The plugin package under plugins/beads/ is separate from bd setup codex. The setup command writes a small setup-only skill and managed guidance into the target repository or user-level .agents directory.
In worktree/shared/BEADS_DIR setups, use bd where to confirm the resolved workspace; the integration does not require a local ./.beads.
bd setup codex uses its own marker pair (BEGIN/END BEADS CODEX SETUP), distinct from the BEGIN/END BEADS INTEGRATION markers used by bd setup factory and bd setup mux. Running both bd setup codex and bd setup factory/mux against the same AGENTS.md will leave two managed sections side by side; each bd setup … --check only inspects its own section, and bd setup … --remove only removes its own section.

Mux

Mux reads layered instruction files, including workspace AGENTS.md. Adding the beads section is enough to get Mux and beads working together.

Installation

bd setup mux            # Root AGENTS.md
bd setup mux --project  # Root AGENTS.md + .mux/AGENTS.md
bd setup mux --global   # Root AGENTS.md + ~/.mux/AGENTS.md

What Gets Installed

Creates or updates AGENTS.md with the beads integration section (same markers as Factory.ai and Codex).

Notes

Mux instruction file behavior is documented at https://mux.coder.com/AGENTS.md.
Restart the workspace session if Mux is already running.

Flags

Flag	Description
`--check`	Check root integration (and with layer flags, also check those layers)
`--remove`	Remove root integration (and with layer flags, also remove those layers)
`--project`	Install/check/remove workspace-layer instructions in `.mux/AGENTS.md`
`--global`	Install/check/remove global-layer instructions in `~/.mux/AGENTS.md`

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 --hook-json when a session starts, resumes, clears, or restarts after compaction

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

Same hooks, but only active for this project

Instruction file (CLAUDE.md in project root):

Minimal-profile beads section pointing to bd prime
Managed with hash/version markers for safe updates and --check freshness detection

Flags

Flag	Description
`--check`	Check both hooks and the managed `CLAUDE.md` beads section
`--remove`	Remove beads hooks and managed `CLAUDE.md` beads section
`--project`	Install for this project only (not globally)
`--stealth`	Use `bd prime --stealth` (flush only, no git operations)

Examples

# Check hooks + CLAUDE.md beads section
bd setup claude --check
# Output: ✓ Global hooks installed: /Users/you/.claude/settings.json
#         ✓ Claude Code integration installed: /path/to/CLAUDE.md (current)

# Remove hooks
bd setup claude --remove

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

How It Works

The hook calls bd prime --hook-json which:

Outputs workflow context wrapped in the SessionStart JSON envelope Claude Code expects
Prints persistent memories near the top so hook-output previews do not hide them
Starts with a truncation warning telling agents to read the full persisted hook output when the host caps previews
Ensures Claude always knows how to use beads
Follows resolved workspace semantics, so bd where is the right diagnostic check when local ./.beads is absent

For low-token hooks that only need durable project facts, use bd prime --memories-only.

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

Gemini CLI

Gemini CLI integration uses a SessionStart hook to automatically inject beads workflow context when a session opens.

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 --hook-json when a new session starts, wrapped in the JSON envelope Gemini's hook contract requires

Project installation (.gemini/settings.json):

Same hooks, but only active for this project

Instruction file (GEMINI.md in project root):

Minimal-profile beads section pointing to bd prime
Managed with hash/version markers for safe updates and --check freshness detection

Flags

Flag	Description
`--check`	Check both hooks and the managed `GEMINI.md` beads section
`--remove`	Remove beads hooks and managed `GEMINI.md` beads section
`--project`	Install for this project only (not globally)
`--stealth`	Use `bd prime --stealth` (flush only, no git operations)

Examples

# Check hooks + GEMINI.md beads section
bd setup gemini --check
# Output: ✓ Global hooks installed: /Users/you/.gemini/settings.json
#         ✓ Gemini CLI integration installed: /path/to/GEMINI.md (current)

# 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:

Outputs workflow context for Gemini to read
Prints persistent memories near the top so hook-output previews do not hide them
Starts with a truncation warning telling agents to read the full persisted hook output when the host caps previews
Ensures Gemini always knows how to use beads

For low-token hooks that only need durable project facts, use bd prime --memories-only.

This works similarly to Claude Code integration, using Gemini CLI's hook system (SessionStart event). Unlike Claude Code, Gemini requires hook stdout to be valid JSON — bd prime --hook-json wraps the markdown in the required envelope.

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 dolt push 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 --claim

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

Comparison

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

Best Practices

Start with Factory integration - Creates AGENTS.md which works across multiple AI tools:
```
bd setup factory
```
Add tool-specific integrations as needed - Claude hooks, Cursor rules, or Aider config for tool-specific features
Install globally for Claude Code or Gemini CLI - You'll get beads context in every project automatically
Use stealth mode in CI/CD - bd setup claude --stealth or bd setup gemini --stealth avoids git operations that might fail in automated environments
Commit instruction files to git - This ensures all team members and AI tools get the same instructions (AGENTS.md, CLAUDE.md, GEMINI.md, as applicable)

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"

Restart your AI tool after installation
Verify with bd setup <tool> --check
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

Custom Recipes

You can add custom recipes for editors/tools not included in the built-in list.

Adding a Custom Recipe

# Add a recipe that writes to a specific path
bd setup --add myeditor .myeditor/rules.md

# Install it
bd setup myeditor

# Check it
bd setup myeditor --check

# Remove it
bd setup myeditor --remove

User Recipes File

Custom recipes are stored in .beads/recipes.toml:

[recipes.myeditor]
name = "myeditor"
path = ".myeditor/rules.md"
type = "file"

Using Arbitrary Paths

For one-off installs without saving a recipe:

# Write template to any path
bd setup -o .my-custom-location/beads.md

# Inspect the template first
bd setup --print

Recipe Types

Type	Description	Example
`file`	Write template to a single file	cursor, windsurf, cody, kilocode
`hooks`	Modify JSON settings to add hooks	claude, gemini
`section`	Inject marked section into existing file	factory
`multifile`	Write multiple files	aider

Custom recipes added via --add are always type file.

FilesExpand file tree

SETUP.md

Latest commit

History

SETUP.md

File metadata and controls

Setup Command Reference

Overview

bd prime as SSOT

Profiles

Built-in Recipes

Quick Start

Factory.ai (Droid)

Installation

What Gets Installed

AGENTS.md Standard

Flags

Examples

How It Works

Updating Existing AGENTS.md

When to Use This vs Other Integrations

Codex CLI

Installation

What Gets Installed

Flags

Notes

Mux

Installation

What Gets Installed

Notes

Flags

Claude Code

Installation

What Gets Installed

Flags

Examples

How It Works

Gemini CLI

Installation

What Gets Installed

Flags

Examples

How It Works

Cursor IDE

Installation

What Gets Installed

Flags

Examples

How It Works

Aider

Installation

What Gets Installed

Flags

Examples

How It Works

Comparison

Best Practices

Troubleshooting

"Hooks not working"

"Context not appearing"

"Want to switch from global to project hooks"

Custom Recipes

Adding a Custom Recipe

User Recipes File

Using Arbitrary Paths

Recipe Types

Related Documentation

`bd prime` as SSOT