Monorepo Initialization

Monorepo Initialization Skill

Purpose

Systematically initialize AGENTS.md files throughout a monorepo, creating a hierarchical context system where:

• Root AGENTS.md coordinates all agents
• Each package/service has its own AGENTS.md with hierarchy metadata
• All files link back to root CLAUDE.md (philosophy)
• AI agents can navigate context efficiently across packages

This enables large projects to maintain clear, navigable agent guidance without overwhelming token budgets.

When to Use

• New monorepo setup - Initialize entire project structure
• Adding new packages - Run on new subdirectory
• Improving agent context - Refresh existing AGENTS.md files
• Scaling team - Ensure new members understand cross-package dependencies
• Microservices - Document each service's agent context independently

The Problem

Without structured AGENTS.md hierarchy:

• Agents get confused about project structure
• Context is scattered or missing
• Cross-package dependencies aren't clear
• Scaling to 5+ packages becomes difficult
• New team members waste time understanding structure

With this skill:

• Agents understand full project structure
• Each package has focused, actionable guidance
• Dependencies and integration points are documented
• Scales to 20+ packages without confusion

Process

Phase 1: Discovery (5-10 minutes)

Script automatically scans for:

• Project files: package.json, go.mod, Cargo.toml, pyproject.toml, pom.xml
• Directories: src/, lib/, components/, services/
• Config files: .cursorrules, .github/copilot-instructions.md
• Documentation: README.md, docs/

Scoring heuristic:

Project file present:     +10 points
src/lib/components dir:   +5 points
Config file present:      +3 points
>10 source files:         +3 points
README/docs present:      +2 points
Threshold: > 5 points = initialize

Phase 2: Root Analysis

Create root AGENTS.md containing:

• Project overview
• All agents and their modes
• Available commands and skills
• Directory structure index (table of all packages)
• Hierarchy linking explanation

Example:

# Project Agents

## Directory Structure

| Package | Level | Purpose | Key Files |
|---------|-------|---------|-----------|
| `packages/api` | API Services | REST backend | src/routes/, src/models/ |
| `packages/web` | Frontend | React UI | src/components/, src/pages/ |

## Hierarchy Linking

Each package maintains its own AGENTS.md with:
- **Hierarchy Level**: Role in system (e.g., "API Services")
- **Parent**: Link to this AGENTS.md
- **Philosophy**: Link to CLAUDE.md

See individual AGENTS.md files for package-specific guidance.

Phase 3: Package Initialization

For each important subdirectory, create localized AGENTS.md (~20 lines):

Metadata (Required per Anthropic hierarchy docs):

---
hierarchy:
  level: "API Services"
  parent: "../AGENTS.md"
  philosophy: "../../CLAUDE.md"
---

# API Service Agents

Content:

• Framework/tech stack used
• Build/lint/test commands with examples
• Code style guidelines (imports, formatting, naming)
• Common patterns specific to this package
• Integration points with other packages
• Key files and their purposes

Example for API package:

# API Service Agents

**Hierarchy Level**: API Services (REST backend, database layer)  
**Parent**: [../AGENTS.md](../AGENTS.md)  
**Philosophy**: [CLAUDE.md](../../CLAUDE.md)

## Tech Stack

- Express.js (server framework)
- TypeScript (type safety)
- Prisma (ORM)
- PostgreSQL (database)

## Key Commands

```bash
# Development
npm run dev              # Start dev server on :3000
npm run build            # Compile TypeScript
npm run test             # Run Jest tests
npm run test:watch       # Watch mode

# Single test example
npm test -- routes.test.ts

# Linting & formatting
npm run lint             # ESLint check
npm run format           # Prettier format

Code Style

Imports: Absolute paths from src/, relative for same package

import { UserService } from '@api/services'  // Cross-package
import { helper } from '../utils'             // Local

Naming: camelCase functions, PascalCase classes, UPPER_SNAKE_CASE constants

Types: Explicit return types for all functions, use Zod for runtime validation

Patterns

• Services: Business logic in /services, thin controllers
• Models: Prisma schemas in /prisma/schema.prisma
• Error handling: Use custom AppError class with status codes
• Logging: Use logger instance (shared/logger)

Integration Points

• Web package: Uses /api/* routes via fetch
• Shared package: Uses types and utilities from shared
• Database: Migrations in /prisma/migrations

AI Agent Guidance

For Claude/GPT working in this package:

1. Follow Express.js patterns (middleware, routing)
2. Always add types (no any)
3. Write tests alongside features
4. Update Prisma schema, run migrations
5. Reference /shared for shared types/utilities

### Phase 4: Root CLAUDE.md Update

Update (or create) root CLAUDE.md to document the hierarchy:

```markdown
# Project Philosophy

[Your guiding principles and vision...]

## Agent Coordination

See **[AGENTS.md](./AGENTS.md)** for:
- Agents and their modes (plan/build/review)
- Available commands and skills
- Directory context index

This CLAUDE.md defines **philosophy**. AGENTS.md documents **agents and tools**.

## Agent Contexts (Hierarchical)

Each package/service maintains specialized agent context:

| Directory | AGENTS.md | Level | Purpose |
|-----------|-----------|-------|---------|
| Root | [AGENTS.md](./AGENTS.md) | Coordination | Project overview, cross-package agents |
| `packages/api` | [packages/api/AGENTS.md](./packages/api/AGENTS.md) | API Services | REST backend, database layer |
| `packages/web` | [packages/web/AGENTS.md](./packages/web/AGENTS.md) | Frontend | React UI, styling, client logic |
| `packages/shared` | [packages/shared/AGENTS.md](./packages/shared/AGENTS.md) | Shared Utilities | Types, helpers, common code |

Each subdirectory's AGENTS.md includes hierarchy metadata:
- **Hierarchy Level**: Role in system architecture
- **Parent**: Link to parent AGENTS.md for coordination
- **Philosophy**: Link to this CLAUDE.md for guiding principles

This three-tier system (philosophy → coordination → specialization) allows AI agents to:
1. Understand project vision and values (CLAUDE.md)
2. Understand cross-package structure (root AGENTS.md)
3. Get specialized guidance for their specific package (package AGENTS.md)

Phase 5: Verification & Cleanup

Verify all links work:

✓ Root AGENTS.md exists and links to all packages
✓ Root CLAUDE.md lists all AGENTS.md files
✓ Each package AGENTS.md has hierarchy metadata
✓ No broken relative paths
✓ Build commands are tested (where applicable)

Cleanup:

git add .
git commit -m "chore: initialize monorepo AGENTS.md hierarchy"

Usage

CLI (from root):

# Initialize entire project (interactive)
/monorepo-initialization

# Dry-run: preview without changes
/monorepo-initialization --dry-run

# Initialize with specific depth
/monorepo-initialization --depth=3

# Re-initialize (overwrite existing)
/monorepo-initialization --preserve=false

# Initialize specific directory
/monorepo-initialization packages/my-new-service

OpenCode:

use_skill("monorepo-initialization", {
    "depth": 2,
    "dry_run": False,
    "preserve": False
})

Claude Code:

Use monorepo-initialization skill to set up AGENTS.md hierarchy for new packages

Options

Directory Scoring

Automatically scores directories to determine importance:

Only directories scoring > 5 are initialized (configurable via --min-score).

Output Example

🔍 Scanning monorepo structure...
📊 Found 8 directories above threshold (score > 5)

📁 Root
   ✓ AGENTS.md created (project coordination, 8 packages)
   ✓ CLAUDE.md updated (hierarchy linking)

📦 Batch 1/3: [packages/api, packages/web, packages/shared]
   ✓ packages/api: AGENTS.md (Express.js, TypeScript, Prisma)
   ✓ packages/web: AGENTS.md (Next.js 14, React, Tailwind)
   ✓ packages/shared: AGENTS.md (TypeScript utilities, types)

📦 Batch 2/3: [packages/cli, packages/docs, services/worker]
   ✓ packages/cli: AGENTS.md (TypeScript CLI, Yargs)
   ✓ packages/docs: AGENTS.md (MDX docs site, Nextra)
   ✓ services/worker: AGENTS.md (Bull queue, async jobs)

📦 Batch 3/3: [.claude, scripts]
   ✓ .claude: AGENTS.md (custom Claude Code hooks)
   ✓ scripts: AGENTS.md (utility scripts, Bash)

✅ Summary: 1 root + 8 packages initialized
   📚 All packages linked hierarchically to CLAUDE.md
   🔗 Cross-package dependencies documented
   💾 Git commit ready: "chore: initialize monorepo AGENTS.md hierarchy"

What Gets Created

For each important directory:

my-monorepo/
├── AGENTS.md                    ← Root coordination
├── CLAUDE.md                    ← Updated with hierarchy
├── packages/
│   ├── api/
│   │   ├── AGENTS.md            ← New (API Services level)
│   │   └── src/
│   ├── web/
│   │   ├── AGENTS.md            ← New (Frontend level)
│   │   └── src/
│   ├── shared/
│   │   ├── AGENTS.md            ← New (Shared Utilities level)
│   │   └── src/
│   └── cli/
│       ├── AGENTS.md            ← New (CLI Tools level)
│       └── src/

Each AGENTS.md includes:

• Hierarchy metadata (level, parent, philosophy)
• Tech stack summary
• Build/test/lint commands
• Code style guidelines
• Common patterns
• Integration points
• AI agent guidance

Quality Checklist

Before running this skill, verify:

• Root CLAUDE.md exists or will be created
• Project structure is stable (won't add/remove packages soon)
• Key dependencies between packages are known

After running, verify:

• Each AGENTS.md is 15-25 lines (focused, not overwhelming)
• All hierarchy metadata is correct
• Links are valid (no broken references)
• Build commands are accurate
• Cross-package dependencies are noted
• Git commit message is clear

Best Practices

1. Run once per new package - Update root AGENTS.md when adding packages
2. Keep AGENTS.md lean - ~20 lines per file, link to docs for details
3. Update when tech changes - Refresh AGENTS.md if framework/language updates
4. Link to packages - Reference package-specific docs, not inline docs
5. Verify the hierarchy - Test that agents can navigate from root → package

Common Patterns

Adding a new package:

# Add your new package directory
mkdir -p packages/my-service/src

# Re-run monorepo-initialization
/monorepo-initialization

# Verifies all links still work, updates root AGENTS.md

Migrating existing project:

# Run on project with existing AGENTS.md files
/monorepo-initialization --preserve=true

# Won't overwrite existing files, just adds missing ones

Large monorepos (20+ packages):

# Increase recursion depth, process in batches
/monorepo-initialization --depth=3 --batch-size=5 --min-score=7

# Higher score = fewer but more important directories initialized

Success Metrics

After running:

• ✓ Root AGENTS.md exists and lists all packages
• ✓ All important directories have AGENTS.md
• ✓ Each AGENTS.md has hierarchy metadata
• ✓ CLAUDE.md links to package AGENTS.md files
• ✓ AI agents can understand project structure
• ✓ New team members can navigate contexts easily
• ✓ Cross-package dependencies are clear

This transforms your monorepo from "confusing structure" to "clear, navigable context for AI agents and humans alike."

Anti-Rationalization Table