🧭 Atlas: Replace hand-written API routes with generated list from OpenAPI

[ToolchainLab]

• 💡 What: Replaced hand-written API routes in README with a generated list from OpenAPI, delimited by <!-- BEGIN ROUTES --> and <!-- END ROUTES -->.
• 🎯 Why: Prevents documentation drift and ensures route list is perfectly synchronized with the codebase's actual capabilities. Hand-written sections diverge over time.
• 🔬 Verification: uv run scripts/check_doc_routes.py passes successfully, validating the README.md.
• 🔒 Drift Prevention: CI runs check_doc_routes.py which fails if the auto-generated API list in the README differs from actual application routes.
• 🗺️ Evidence: Verified source of truth uses app.openapi().get("paths", {}) logic in scripts/check_doc_routes.py.

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PR created automatically by Jules for task 2060591708496536493 started by @ToolchainLab

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