How I Structure CLAUDE.md After 1000+ Sessions

The best way to structure CLAUDE.md is with a layered system: identity at the top, behavioral rules in the middle, and reference paths at the bottom. After 1000+ Claude Code sessions, I settled on a pattern that keeps the file under 200 lines while giving the agent everything it needs. The key insight is that CLAUDE.md is not documentation. It is runtime instructions. Every line should change how the agent behaves. If a line does not change behavior, delete it. I organize mine into five sections: Core Identity (who the agent is and what it does), Behavioral Rules (DO/DON'T lists), Autonomy Levels (when to ask vs act), Key Paths (where to find things), and Reference Links (load-on-demand docs). This structure scales from solo projects to multi-agent systems.