Deep Init Skill

Creates comprehensive, hierarchical AGENTS.md documentation across the entire codebase.

Core Concept

AGENTS.md files serve as AI-readable documentation that helps agents understand:

• What each directory contains
• How components relate to each other
• Special instructions for working in that area
• Dependencies and relationships

Hierarchical Tagging System

Every AGENTS.md (except root) includes a parent reference line:

**Parent context:** `../AGENTS.md`

This MUST be visible prose, never an HTML comment. Claude Code strips HTML

comments before a memory file reaches the model, so <!-- Parent: ... -->,

<!-- Generated: ... --> and a commented MANUAL boundary are invisible to the

agent that is supposed to act on them.

This creates a navigable hierarchy:

/AGENTS.md                          ← Root (no parent line)
├── src/AGENTS.md                   ← **Parent context:** `../AGENTS.md`
│   ├── src/components/AGENTS.md    ← **Parent context:** `../AGENTS.md`
│   └── src/utils/AGENTS.md         ← **Parent context:** `../AGENTS.md`
└── docs/AGENTS.md                  ← **Parent context:** `../AGENTS.md`

Loading Model

Stock Claude Code discovers nested CLAUDE.md by basename and never loads a

nested AGENTS.md; a root @AGENTS.md import does not reach subdirectories

either. The nested files generated here are delivered by OMC's PostToolUse

directory-context injector, which walks up from each accessed file and injects

the nearest AGENTS.md/README.md once per session.

That means the hierarchy requires OMC's hooks to be active. When OMC hooks are

disabled (DISABLE_OMC=1, OMC_SKIP_HOOKS=post-tool-use) or the plugin is not

registered, add a root-level CLAUDE.md symlink or @AGENTS.md import for the

root file and expect nested files to stay unread.

AGENTS.md Template

# {Directory Name}

**Parent context:** `{relative_path_to_parent}/AGENTS.md`
**Generated:** {timestamp} · **Updated:** {timestamp}

## Purpose
{One-paragraph description of what this directory contains and its role}

## Key Files
{List each significant file with a one-line description}

| File | Description |
|------|-------------|
| `file.ts` | Brief description of purpose |

## Subdirectories
{List each subdirectory with brief purpose}

| Directory | Purpose |
|-----------|---------|
| `subdir/` | What it contains (see `subdir/AGENTS.md`) |

## For AI Agents

### Working In This Directory
{Special instructions for AI agents modifying files here}

### Testing Requirements
{How to test changes in this directory}

### Common Patterns
{Code patterns or conventions used here}

## Dependencies

### Internal
{References to other parts of the codebase this depends on}

### External
{Key external packages/libraries used}

## Manual Notes

Notes under this heading are written by humans and preserved on regeneration.

Execution Workflow

Step 1: Map Directory Structure

Task(subagent_type="explore", model="haiku",
  prompt="List all directories recursively. Exclude: node_modules, .git, dist, build, __pycache__, .venv, coverage, .next, .nuxt")

Step 2: Create Work Plan

Generate todo items for each directory, organized by depth level:

Level 0: / (root)
Level 1: /src, /docs, /tests
Level 2: /src/components, /src/utils, /docs/api
...

Step 3: Generate Level by Level

IMPORTANT: Generate parent levels before child levels to ensure parent references are valid.

For each directory:

1. Read all files in the directory
2. Analyze purpose and relationships
3. Generate AGENTS.md content
4. Write file with proper parent reference

Step 4: Compare and Update (if exists)

When AGENTS.md already exists:

1. Read existing content
2. Identify sections:

• Auto-generated sections (can be updated)
• Manual sections (the ## Manual Notes heading and everything under it are preserved)

1. Compare:

• New files added?
• Files removed?
• Structure changed?

1. Merge:

• Update auto-generated content
• Preserve manual annotations
• Update timestamp

Step 5: Validate Hierarchy

After generation, run validation checks:

Validation script pattern:

# Find all AGENTS.md files
find . -name "AGENTS.md" -type f

# Check parent references
grep -r "\*\*Parent context:\*\*" --include="AGENTS.md" .

Smart Delegation

Empty Directory Handling

When encountering empty or near-empty directories:

Example minimal AGENTS.md for directory-only containers:

# {Directory Name}

**Parent context:** `../AGENTS.md`

## Purpose
Container directory for organizing related modules.

## Subdirectories
| Directory | Purpose |
|-----------|---------|
| `subdir/` | Description (see `subdir/AGENTS.md`) |

Parallelization Rules

1. Same-level directories: Process in parallel
2. Different levels: Sequential (parent first)
3. Large directories: Spawn dedicated agent per directory
4. Small directories: Batch multiple into one agent

Quality Standards

Must Include

• [ ] Accurate file descriptions
• [ ] Correct parent references
• [ ] Subdirectory links
• [ ] AI agent instructions

Must Avoid

• [ ] Generic boilerplate
• [ ] Incorrect file names
• [ ] Broken parent references
• [ ] Missing important files

Example Output

Root AGENTS.md

# my-project

**Generated:** 2024-01-15 · **Updated:** 2024-01-15

## Purpose
A web application for managing user tasks with real-time collaboration features.

## Key Files
| File | Description |
|------|-------------|
| `package.json` | Project dependencies and scripts |
| `tsconfig.json` | TypeScript configuration |
| `.env.example` | Environment variable template |

## Subdirectories
| Directory | Purpose |
|-----------|---------|
| `src/` | Application source code (see `src/AGENTS.md`) |
| `docs/` | Documentation (see `docs/AGENTS.md`) |
| `tests/` | Test suites (see `tests/AGENTS.md`) |

## For AI Agents

### Working In This Directory
- Always install dependencies after modifying the project manifest
- Use TypeScript strict mode
- Follow ESLint rules

### Testing Requirements
- Run tests before committing
- Ensure >80% coverage

### Common Patterns
- Use barrel exports (index.ts)
- Prefer functional components

## Dependencies

### External
- React 18.x - UI framework
- TypeScript 5.x - Type safety
- Vite - Build tool

## Manual Notes

Custom project notes can be added under this heading.

Nested AGENTS.md

# components

**Parent context:** `../AGENTS.md`
**Generated:** 2024-01-15 · **Updated:** 2024-01-15

## Purpose
Reusable React components organized by feature and complexity.

## Key Files
| File | Description |
|------|-------------|
| `index.ts` | Barrel export for all components |
| `Button.tsx` | Primary button component |
| `Modal.tsx` | Modal dialog component |

## Subdirectories
| Directory | Purpose |
|-----------|---------|
| `forms/` | Form-related components (see `forms/AGENTS.md`) |
| `layout/` | Layout components (see `layout/AGENTS.md`) |

## For AI Agents

### Working In This Directory
- Each component has its own file
- Use CSS modules for styling
- Export via index.ts

### Testing Requirements
- Unit tests in `__tests__/` subdirectory
- Use React Testing Library

### Common Patterns
- Props interfaces defined above component
- Use forwardRef for DOM-exposing components

## Dependencies

### Internal
- `src/hooks/` - Custom hooks used by components
- `src/utils/` - Utility functions

### External
- `clsx` - Conditional class names
- `lucide-react` - Icons

## Manual Notes

Triggering Update Mode

When running on an existing codebase with AGENTS.md files:

1. Detect existing files first
2. Read and parse existing content
3. Analyze current directory state
4. Generate diff between existing and current
5. Apply updates while preserving manual sections

Performance Considerations

• Cache directory listings - Don't re-scan same directories
• Batch small directories - Process multiple at once
• Skip unchanged - If directory hasn't changed, skip regeneration
• Parallel writes - Multiple agents writing different files simultaneously