How to Organize Large Projects for Claude Code

Introduction

Claude Code works brilliantly on small to medium projects. A few dozen files, clear structure, straightforward dependencies. But what happens when your codebase grows to hundreds or thousands of files? When multiple teams contribute code across different domains? When the full context of your project exceeds what any AI can hold in memory?

Large projects present unique challenges for AI-assisted development. Context windows have limits. File discovery becomes a needle-in-haystack problem. Claude can lose focus when overwhelmed with irrelevant information. These are not Claude's shortcomings; they are fundamental constraints that require intentional strategies to overcome.

This guide covers the organizational patterns, documentation strategies, and workflow techniques that make Claude Code effective at scale. Whether you are maintaining a legacy monolith, building a sprawling microservices architecture, or coordinating work across a large team, these approaches will help you get consistent, high-quality results from Claude.

The key insight: scaling Claude Code is not about giving it more context. It is about giving it better context, the right information at the right time, structured for immediate comprehension.

Challenges with Large Codebases

Before diving into solutions, it helps to understand exactly why large projects are difficult for AI assistants. These challenges inform every strategy that follows.

Context Limits Are Real

Every AI model has a context window, a maximum amount of text it can consider at once. While these windows have grown substantially, they remain finite. A large codebase can easily exceed this limit, meaning Claude cannot see everything simultaneously.

When context is limited, Claude must make decisions based on incomplete information. It might suggest a pattern that conflicts with code it has not seen, or miss existing utilities that would solve the problem. The solution is not to somehow expand context, but to ensure the most relevant context is always available.

File Discovery Becomes Difficult

In a small project, Claude can quickly scan all files to understand the codebase. In a large project, this approach breaks down. With thousands of files, Claude cannot read everything, so it must decide which files matter for the current task.

Poor organization makes this worse. If your authentication logic is scattered across auth/, middleware/, utils/auth/, and legacy/auth-old/, Claude has no reliable way to find all relevant code. It will find some, miss some, and produce inconsistent results.

Lost Focus and Drift

Large projects often involve complex, multi-step tasks. As Claude works through these tasks, it can lose track of the original goal, introduce inconsistencies, or make decisions that conflict with earlier choices. This "drift" becomes more pronounced as project complexity increases.

The antidote is structure. Clear boundaries, explicit documentation, and well-defined modules help Claude maintain focus even during extended work sessions.

Strategic CLAUDE.md

In small projects, CLAUDE.md can contain detailed instructions for every aspect of development. In large projects, this approach backfires. A 2,000-line instruction file consumes context that should go to actual code, and Claude may not internalize all of it anyway.

High-Level Overview Only

Your root CLAUDE.md should provide orientation, not exhaustive detail. Think of it as the introduction chapter of a book, enough to understand the overall story without revealing every plot point.

# Project Overview
E-commerce platform with web, mobile, and admin interfaces.
Monorepo structure with shared packages.

# Architecture
- /apps/web - Customer-facing Next.js application
- /apps/admin - Internal admin dashboard
- /apps/mobile - React Native mobile app
- /packages/shared - Shared types, utils, and components
- /packages/api-client - Generated API client
- /services/api - Node.js backend services

# Key Conventions
- TypeScript everywhere, strict mode
- All API calls through api-client package
- Shared types in packages/shared/types
- See each directory's README for specific patterns

# What NOT to Do
- Never modify packages/api-client directly (generated)
- Never import from apps/ into packages/
- Never bypass api-client for direct fetch calls

Defer to Local Documentation

Instead of documenting every subsystem in the root CLAUDE.md, point Claude to local documentation. This keeps the root file focused while ensuring detailed guidance exists where it is needed.

# Documentation Structure
Each major directory contains its own README with:
- Directory purpose and scope
- Local conventions and patterns
- Examples of correct usage
- Common pitfalls to avoid

When working in a directory, read its README first.

Focus on Boundaries

The most important information in a large project is what connects to what. Which packages depend on which? Which services call which APIs? What data flows where? Document boundaries and interfaces, not implementation details.

Folder-Level Documentation

The solution to context limits is distributed documentation. Each major directory gets its own README that Claude reads when working in that area. This ensures relevant context is always available without overwhelming the root configuration.

README Per Major Directory

Every significant directory should contain a README.md that explains its purpose, patterns, and conventions. When Claude works in that directory, it naturally discovers this documentation.

src/
  auth/
    README.md           # Auth-specific patterns
    login.ts
    session.ts
  payments/
    README.md           # Payment-specific patterns
    checkout.ts
    subscriptions.ts
  notifications/
    README.md           # Notification-specific patterns
    email.ts
    push.ts

What Each README Should Contain

Directory READMEs should answer the questions Claude will have when working in that area.

# Authentication Module

## Purpose
Handles all authentication flows: login, logout, session
management, password reset, and OAuth integrations.

## Key Files
- login.ts - Login flow and credential validation
- session.ts - Session creation, validation, refresh
- oauth.ts - Third-party OAuth providers
- middleware.ts - Express middleware for route protection

## Patterns
- All auth functions return AuthResult type
- Sessions stored in Redis, not database
- Use verifySession() middleware, never raw token checks
- Passwords hashed with bcrypt, cost factor 12

## Dependencies
- Uses: packages/shared/types, services/redis
- Used by: apps/web, apps/api, apps/admin

## Common Tasks
- Adding new OAuth provider: See oauth.ts OAuthProvider interface
- Modifying session duration: See session.ts SESSION_CONFIG
- Adding new protected route: Apply verifySession middleware

Keep Documentation Current

Stale documentation is worse than no documentation. It actively misleads Claude into producing incorrect code. Build documentation updates into your workflow: when patterns change, READMEs update.

Modular Architecture

Clear architectural boundaries are not just good engineering practice; they are essential for effective AI assistance. When modules have well-defined responsibilities and interfaces, Claude can work confidently within one module without needing to understand the entire system.

Clear Boundaries Claude Can Understand

Each module should have an obvious purpose that Claude can infer from its name and structure. Avoid modules that do "a little bit of everything" or have unclear responsibilities.

• Good: payments/ - Handles all payment processing
• Good: notifications/ - Sends emails, SMS, push notifications
• Bad: helpers/ - Random utility functions
• Bad: common/ - Shared code without clear theme

Explicit Interfaces Between Modules

When modules communicate, they should do so through explicit interfaces. This makes dependencies visible and helps Claude understand how pieces connect.

// payments/index.ts - Public interface
export { processPayment } from './checkout';
export { createSubscription } from './subscriptions';
export type { PaymentResult, SubscriptionPlan } from './types';

// Everything else is internal implementation

Encapsulated Implementation Details

Internal module details should stay internal. When Claude works in the payments module, it should not need to understand how notifications work internally, only how to call the notification service.

// In payments/checkout.ts
import { sendReceipt } from '../notifications';

// Good: Use the public interface
await sendReceipt(order.email, receipt);

// Bad: Reach into notification internals
import { emailClient } from '../notifications/email/client';
await emailClient.send({ ... });

Self-Contained Feature Modules

Where possible, organize by feature rather than by layer. A feature module contains everything related to that feature: components, services, types, and tests. This locality makes it easier for Claude to find all relevant code.

features/
  checkout/
    components/
      CheckoutForm.tsx
      PaymentMethod.tsx
    hooks/
      useCheckout.ts
    services/
      checkoutService.ts
    types/
      checkout.ts
    tests/
      checkout.test.ts
    README.md

Selective Context

The most powerful technique for large projects is explicitly telling Claude which parts to focus on. Rather than letting Claude guess what is relevant, you direct its attention to specific areas.

Tell Claude Which Parts to Focus On

When starting a task, specify exactly which directories, files, or modules are relevant. This prevents Claude from wasting context on irrelevant code.

I need to add a new payment method to the checkout flow.

Relevant code is in:
- src/features/checkout/
- src/services/payments/
- src/types/payment.ts

You can ignore all other directories for this task.

Scope Tasks Explicitly

Large projects benefit from explicit task scoping. Tell Claude not just what to do, but what the boundaries of the task are.

Add Apple Pay support to the checkout flow.

Scope:
- Add ApplePay component in checkout/components/
- Add payment method type to types/payment.ts
- Integrate with existing checkoutService

Out of scope:
- Backend changes (separate task)
- Other payment methods
- Mobile app (web only for now)

Reference Specific Files

When asking Claude to follow existing patterns, point to specific examples rather than asking it to find them.

Add a new CreditCard component following the same pattern
as checkout/components/PayPal.tsx.

Match the structure, prop types, and error handling
approach used in that file.

Break Large Tasks into Focused Steps

Instead of asking Claude to implement an entire feature, break it into steps that each focus on a specific area. This keeps context focused and results more consistent.

Step 1: "Add ApplePay type to types/payment.ts"
Step 2: "Create ApplePay component in checkout/components/"
Step 3: "Integrate ApplePay into CheckoutForm"
Step 4: "Add tests for ApplePay component"

Using .claudeignore

Just as .gitignore tells Git which files to skip, you can use similar patterns to tell Claude which files are irrelevant. While Claude Code does not have an official .claudeignore file, you can achieve similar results through documentation and explicit instructions.

Exclude Irrelevant Files

Some files and directories are never relevant to development tasks. Generated code, build artifacts, vendored dependencies, and legacy code that should not be modified can all be excluded from Claude's attention.

# Directories to Ignore
The following directories should not be read or modified:

- /dist/ - Build output, generated
- /node_modules/ - Dependencies
- /generated/ - Auto-generated API clients
- /legacy/ - Deprecated code, do not reference
- /vendor/ - Third-party code, do not modify
- *.min.js - Minified files
- *.map - Source maps

Mark Generated Code

Generated files should be clearly marked so Claude knows not to modify them directly. Use comments at the top of generated files and document generation patterns.

/**
 * AUTO-GENERATED FILE - DO NOT MODIFY
 * Generated by: scripts/generate-api-client.ts
 * Source: api/openapi.yaml
 *
 * To update: run `npm run generate:api`
 */

Separate Active from Archived Code

If your project has legacy code that should not be referenced for new development, separate it clearly. Move it to a /legacy/ or /deprecated/ directory and document that Claude should not use it as a pattern source.

# Legacy Code
The /legacy/ directory contains old code maintained for
backward compatibility. Do NOT:
- Reference these files for patterns
- Import from legacy into new code
- Suggest similar approaches

When you see legacy patterns elsewhere, suggest refactoring
to current patterns instead.

Team Coordination

When multiple developers use Claude Code on the same project, coordination becomes essential. Without shared conventions, each developer's Claude sessions may produce inconsistent code, conflicting patterns, or redundant implementations.

Multiple Developers Using Claude Code

Each developer's Claude session starts fresh without knowledge of other developers' work. This means the same question might get different answers depending on who asks and when. Shared documentation and conventions reduce this inconsistency.

Shared CLAUDE.md in Version Control

Your CLAUDE.md and directory READMEs should be version controlled alongside your code. When developers pull the latest changes, they also get the latest AI instructions. This keeps everyone's Claude sessions aligned.

# When updating conventions
1. Update relevant README or CLAUDE.md
2. Include documentation change in the same PR as code change
3. Review documentation changes as carefully as code changes
4. Ensure all developers pull before starting new Claude sessions

Documenting Team Decisions

When the team makes architectural decisions, document them where Claude will find them. This prevents Claude from suggesting approaches the team has explicitly rejected.

# Architectural Decisions

## State Management
We use Zustand, not Redux. This was decided in ADR-005.
Do not suggest Redux patterns or migrations.

## Styling
We use Tailwind CSS with custom design tokens.
Do not suggest CSS-in-JS, styled-components, or similar.

## Testing
We use Vitest with Testing Library.
Do not suggest Jest or Enzyme patterns.

Handling Conflicts

When Claude's suggestions conflict with existing code or another developer's recent work, the documentation should provide clear guidance on which pattern wins.

# When You See Conflicting Patterns
This codebase has some inconsistency from rapid growth.
When you see conflicting patterns:

1. Check the relevant directory README for the current standard
2. If no README guidance, prefer the pattern in newer files
3. If still unclear, ask before implementing

Do not perpetuate old patterns just because they exist.

Review AI-Generated Code

All AI-generated code should go through the same review process as human-written code. Code review catches inconsistencies, ensures patterns are followed, and maintains quality standards regardless of who (or what) wrote the code.

Conclusion

Large projects require intentional organization to work well with Claude Code. The strategies in this guide share a common theme: replace implicit knowledge with explicit documentation, replace sprawling context with focused attention, and replace hope with structure.

The core principles to remember:

• Strategic documentation: Keep root CLAUDE.md high-level; distribute details to directory READMEs
• Clear boundaries: Modular architecture creates natural context zones
• Selective focus: Tell Claude exactly which code matters for each task
• Explicit exclusion: Document what Claude should ignore
• Team alignment: Shared, version-controlled documentation keeps everyone's Claude sessions consistent

These approaches scale with your project. Whether you have 500 files or 50,000, the principles remain the same: give Claude the right context, in the right structure, at the right time.

Start with one improvement. Add directory READMEs to your most active modules. Slim down your root CLAUDE.md. Mark generated files clearly. Each incremental improvement makes Claude more effective and your development faster.

Large projects are complex by nature, but they need not be chaotic. With thoughtful organization, Claude Code becomes a powerful ally at any scale.