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 # Table of contents
 
 - [Welcome](README.md)
+
+## Core Concepts
+
+- [What is Atom?](core-concepts/what-is-atom.md)
+- [Atoms and Modules](core-concepts/atoms-and-modules.md)
+- [Lazy Evaluation and Purity](core-concepts/lazy-evaluation-and-purity.md)
+- [Dependency Management](core-concepts/dependency-management.md)
+
+## Getting Started
+
+- [Installation](getting-started/installation.md)
+- [Your First Atom](getting-started/your-first-atom.md)
+- [Atom Composition](getting-started/atom-composition.md)
+
+## Atom Structure
+
+- [Manifest File (atom.toml)](atom-structure/manifest-file.md)
+- [Module Structure](atom-structure/module-structure.md)
+- [Public and Private Interfaces](atom-structure/public-and-private-interfaces.md)
+
+## Advanced Usage
+
+- [Mono-repo Management](advanced-usage/mono-repo-management.md)
+- [Remote Dependencies](advanced-usage/remote-dependencies.md)
+- [Vendoring](advanced-usage/vendoring.md)
+- [Static Analysis](advanced-usage/static-analysis.md)
+
+## Best Practices
+
+- [Code Organization](best-practices/code-organization.md)
+- [Dependency Management](best-practices/dependency-management.md)
+- [Performance Optimization](best-practices/performance-optimization.md)
+
+## Tooling
+
+- [CLI Tools](tooling/cli-tools.md)
+- [Editor Integration](tooling/editor-integration.md)
+- [CI/CD Integration](tooling/ci-cd-integration.md)
+
+## API Reference
+
+- [Core Functions](api-reference/core-functions.md)
+- [Utility Functions](api-reference/utility-functions.md)
+
+## Tutorials
+
+- [Building a NixOS Configuration](tutorials/building-nixos-configuration.md)
+- [Creating a Reusable Library](tutorials/creating-reusable-library.md)
+- [Managing a Large Project](tutorials/managing-large-project.md)
+
+## Migration Guides
+
+- [From Nix Flakes](migration-guides/from-nix-flakes.md)
+- [From Traditional Nix](migration-guides/from-traditional-nix.md)
+
+## Community and Support
+
+- [Contributing to Atom](community-and-support/contributing.md)
+- [Reporting Issues](community-and-support/reporting-issues.md)
+- [Community Resources](community-and-support/community-resources.md)
+
+## FAQ
+
+- [General Questions](faq/general-questions.md)
+- [Technical Questions](faq/technical-questions.md)
+
+## Appendix
+
+- [Glossary](appendix/glossary.md)
+- [Comparison with Other Systems](appendix/comparison.md)