File	What It Explains
ai-agent.md	How the AI agent works — the three-phase code scanning pipeline, the Gemini integration, the chat system, and the website scanner AI layer
architecture.md	How the full system is structured — all layers from the FastAPI app down to the database, and a step-by-step trace of a real request
api-reference.md	Every API endpoint, its request/response shape, and error codes

Where to Start

If you want to understand how the AI works → ai-agent.md

If you want to understand how the system is structured → architecture.md

If you're looking for a specific endpoint → api-reference.md