Documentation First Setup

Documentation-First Setup

Overview

The Documentation-First Setup Skill creates and maintains comprehensive documentation that helps agents navigate code effectively. Agents navigate codebases via semantic search and tree-walking. Without good docs, they get lost, make assumptions, and produce lower-quality work. Humans traditionally don't maintain documentation because it's tedious. But agents should do it—their time is cheaper than ours.

Core principle: Well-documented code lets agents navigate independently and make architecture-aware decisions. Poorly documented code makes agents ask basic questions instead of shipping features.

Dependency: Claude Code CLI with access to read files and create documentation.

When to Use

• New project setup: Establish documentation foundations from day one
• Onboarding new agents: Before assigning complex tasks
• After significant refactors: Update documentation to reflect new structure
• Before parallel work: Ensure agents have clear understanding of architecture
• Code review time: When you notice agents are confused about how things work
• Quarterly maintenance: Refresh documentation to match current codebase state

When NOT to Use

• Small, trivial projects (single file, obvious structure)
• When nobody will ever touch the code again
• For third-party or generated code (document around it, not within it)

Common Mistakes

| Mistake | Why it's wrong | |---------|---------------| | Over-documenting obvious things | "The User class represents a user" wastes time. Focus on why and how, not what. | | Not documenting design decisions | Agents and humans both ask "why is this structured this way?" Design decisions are the most valuable documentation. | | Letting documentation drift | Docs that don't match code become lies. Update docs as part of code changes, not later. | | Making READMEs longer than code | If your README is longer than the code, you're documenting the wrong things. | | Orphaning cross-references | If A mentions B, B should mention A. If links are broken, documentation becomes useless. |

The Documentation Process

Step 1: Scan Directory Structure

Start by understanding what we're documenting:

find [target-directory] -type f -name "*.py" -o -name "*.js" -o -name "*.ts" -o -name "*.go" | head -50
tree -L 3 -I "node_modules|__pycache__|venv|build"

Document:

• Directory structure: What's in each folder?
• File count: How many files total?
• Technology: What languages/frameworks?

Create a mental map:

Project/
├── src/
│   ├── core/        (core logic)
│   ├── api/         (external interfaces)
│   ├── utils/       (shared utilities)
│   └── models/      (data structures)
├── tests/           (test suite)
├── docs/            (documentation)
└── config/          (configuration)

Step 2: File-Level Documentation

For every significant file that's missing a header comment:

For code files, add a comment block at the top that includes:

1. Module name: Exactly as it appears in imports
2. Purpose: One sentence of what this file does
3. Key responsibilities: 3-5 bullet points
4. Key design decisions: Why is it structured this way?
5. Related files: Other files this depends on or is used by
6. Usage example: How do you use this module?

Python example:

"""
Module: user_service.py
Purpose: Handles user account management operations

Key responsibilities:
  - User authentication and session management
  - Profile CRUD operations
  - Permission checks and authorization

Key design decisions:
  - Uses dependency injection for database connections
  - Caches user profiles in Redis for 1 hour
  - All database operations are async

Related files:
  - database/user_repository.py: Database access layer
  - auth/jwt_handler.py: Token generation and validation
  - cache/redis_client.py: Cache backend

Usage example:
  service = UserService(db, cache)
  user = await service.get_user(user_id)
"""

JavaScript example:

/**
 * Module: userService.js
 * Purpose: Handles user account management operations
 *
 * Key responsibilities:
 *   - User authentication and session management
 *   - Profile CRUD operations
 *   - Permission checks and authorization
 *
 * Key design decisions:
 *   - Uses dependency injection for database connections
 *   - Caches user profiles in Redis for 1 hour
 *   - All database operations are async (Promises)
 *
 * Related files:
 *   - database/userRepository.js: Database access layer
 *   - auth/jwtHandler.js: Token generation and validation
 *   - cache/redisClient.js: Cache backend
 *
 * Usage example:
 *   const service = new UserService(db, cache);
 *   const user = await service.getUser(userId);
 */

For complex classes/functions, add inline comments explaining "why," not just "what."

Step 3: Folder-Level README.md

For every directory that doesn't have a README.md, create [directory]/README.md:

# [Folder Name]

## Purpose
[One paragraph: What does this folder contain? Why is it organized this way?]

## Structure
What's in this directory:

- **[file/subfolder]**: [One sentence purpose]
- **[file/subfolder]**: [One sentence purpose]

## Architecture Notes
[How do the pieces relate? What's the design philosophy?]

Example for a `src/models/` directory:
- **base.py**: BaseModel abstract class with common patterns
- **user.py**: User model, extends BaseModel
- **team.py**: Team model, extends BaseModel
- **validators.py**: Shared validation functions used by all models

All models follow the Active Record pattern, handle their own validation,
and inherit from BaseModel which provides database save/load functionality.

## How to Use This Folder
[What should developers/agents do when they need something from here?]

When you need to:
- Define a new data model: Create a file here, extend BaseModel
- Add validation: Update validators.py or add model-specific methods
- Work with existing models: Import from the specific model file

## Key Design Decisions
- [Decision 1]: Why did we choose this approach?
- [Decision 2]: What problem does this solve?

## Dependencies
- Depends on: [what this folder uses]
- Used by: [what uses this folder]

## Testing
Tests for this folder are in: `tests/models/`

## Related Folders
- [Related folder]: How it relates
- [Related folder]: How it relates

Step 4: Cross-Reference Documentation

Create (or update) docs/ARCHITECTURE.md or ARCHITECTURE.md at project root:

# Architecture Overview

## System Components

### [Component Name]
Location: `src/component_name/`
Purpose: [What does it do?]
Key files: [List key files]

### [Component Name]
Location: `src/component_name/`
Purpose: [What does it do?]
Key files: [List key files]

## Data Flow
[Describe how data moves through the system]

Example for ML pipeline:

Raw Data (data/raw/) → Preprocessing (src/preprocessing/pipeline.py) → Feature Engineering (src/features/engineer.py) → Training (src/training/train.py) → Evaluation (src/evaluation/metrics.py) → Model Artifacts (models/)

## Key Design Patterns
- [Pattern 1]: Used in [component], solves [problem]
- [Pattern 2]: Used in [component], solves [problem]

## External Dependencies
- [Library]: Used for [purpose], located in [component]
- [Library]: Used for [purpose], located in [component]

## Database Schema
[Link to schema or embed key entity relationships]

## API Endpoints
[Link to API docs or list key endpoints]

## Configuration
Key configuration in: `[location]`
Important settings:
- [Setting]: [What it does]
- [Setting]: [What it does]

## Deployment
[How is this system deployed?]

## Scaling Considerations
[What scales easily? What doesn't? What are the bottlenecks?]

Step 5: Handle Special Cases

For generated code: Don't document individual generated files. Instead, document:

• The generator (what creates these files)
• What the output is for
• How to regenerate
• Any manual customizations to watch for

Example:

# Generated: Database Models (auto-generated)

These files are generated from `schema/models.sql` using SQLAlchemy's declarative generator.

**Generator**: `scripts/generate_models.py`
**Frequency**: Run this whenever you change `schema/models.sql`
**Manual customizations**: None (these are purely generated)

If you need to add business logic to a model, add it to `src/models/mixins/` instead.

For third-party code: Don't document it. Instead, document:

• Why you're using it
• What you're using from it
• Where it's configured
• Any custom extensions

Example:

# FastAPI Configuration
Location: `src/api/app.py`
Third-party: FastAPI (web framework)

We use FastAPI for:
- REST API endpoints
- Request validation
- Automatic OpenAPI docs

Key customizations:
- Custom error handler in `src/api/middleware/error_handler.py`
- JWT authentication middleware in `src/api/middleware/auth.py`

Step 6: Update During Code Changes

When you make code changes:

1. If you rename/move files: Update all references in documentation
2. If you add files: Add file-level header and update folder README
3. If you change architecture: Update ARCHITECTURE.md
4. If you change APIs: Update relevant documentation

Important: Update documentation as part of the code change, not in a separate step.

Step 7: Validation Checklist

Before marking documentation complete:

• [ ] Every .py, .js, .ts, .go file has a header comment explaining purpose
• [ ] Every folder has a README.md
• [ ] ARCHITECTURE.md or docs/ARCHITECTURE.md exists
• [ ] All cross-references are accurate (README links, file mentions, etc.)
• [ ] No "TODO: document this" or similar placeholders
• [ ] Related files links are reciprocal (if A mentions B, B mentions A)
• [ ] Code examples in docs are accurate and would work
• [ ] Configuration and setup instructions are clear
• [ ] A new developer could understand the system from docs + code

Output Format

Provide a summary:

## Documentation Setup Complete

### Files Documented
- [count] Python files
- [count] JavaScript files
- [count] configuration files
- etc.

### Documentation Created
- [ ] File-level headers added to [count] files
- [ ] README.md created for [count] folders
- [ ] ARCHITECTURE.md created or updated
- [ ] Cross-references checked

### Validation
- [count] files with clear header comments
- [count] README.md files in place
- All internal references verified

### Ready for Use
YES - Agents can now navigate this codebase effectively

Configuration Notes

Language-Specific Customization

Python:

# Use """module docstring""" at top of file
# Standard: triple-quoted docstrings following Google/NumPy style

JavaScript/TypeScript:

// Use JSDoc format for files
// /** module docs */ or use TSDoc for TypeScript

Go:

// Use standard Go package documentation format
// godoc will extract these automatically

Project-Specific Customization

1. Add your tech stack to scanning:

`` Add file extensions: .scala, .java, .rs, .rb, etc. ``

1. Customize folder categories:

``` Your project probably has:

• Source code directory (src/, lib/, etc.)
• Test directory (tests/, __tests__, spec/)
• Configuration directory (config/, etc.)
• Docs directory (docs/, doc/, etc.)

Update to match your structure. ```

1. Add required documentation sections:

``` If your project requires:

• Security considerations
• Performance characteristics
• Database migration guides
• Monitoring/logging approach

Add these as required sections in folder READMEs ```

How to Invoke

Run once at project setup:

/documentation-first-setup

Directory: [target directory or "."]

Update after significant changes:

/documentation-first-setup

Directory: src/
Update type: "refresh" (all files) or "new files only"

Tips from Practitioners

When to run this: Best done early in a project, then maintained incrementally. Running it on an existing project can be valuable but requires more effort.

Don't over-document: You don't need multi-paragraph descriptions for simple files. One sentence of purpose + key design decision is often enough.

Make documentation specific: "Handles user data" is bad. "Manages user authentication tokens, validates JWT claims, and handles session expiry" is good. Agents benefit from specificity.

Update as you code: Don't let documentation drift. When you rename a function, update the docs immediately. When you refactor, update the architecture description.

Cross-references matter: When a file references another file, document that relationship. When Agent A looks at file A and doesn't understand it, they should be able to follow the "Related files" link to understand it.

Code examples: Include real usage examples in documentation. Agents and humans both learn faster from concrete examples.

Red flags that documentation is missing:

• Agents ask you "how does X work?" questions
• Agents make assumptions about code structure that are wrong
• Agents spend time reading through code trying to understand relationships
• Documentation would answer these questions

Pro tip: Have agents write documentation about code they encounter. They'll ask good questions and surface ambiguities that humans miss.

Key Principles

1. Documentation enables agent independence. Agents with good docs ship features. Agents without docs ask basic questions.
2. Design decisions are the most valuable docs. Code shows what and how. Documentation explains why.
3. Update docs with code changes. Docs that drift become lies. Update as part of the code change.
4. Be specific and concrete. Agents learn from specific examples and clear relationships, not abstract descriptions.
5. Cross-references reduce navigation overhead. If A depends on B, A should mention B. If A is used by B, B should mention A.

Attribution

Based on techniques from the Coding Agents Lunch & Learn Series. Rob Ennals (Anthropic) contributed the core insight: "The reason why humans don't normally do that is because it's a ton of work. But the great thing about agents is their time is cheaper than ours. So we should just have agents write and maintain documentation."

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: mlopscommunity
• Source: mlopscommunity/Coding-Agents-Conference-skills
• License: Apache-2.0

Install and usage instructions live in the source repository linked above.