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Claude Code shared the generic `json` client format, which the shared configuration reader admits through JSONC parsing with comments and trailing commas enabled. Native Claude Code reads `.claude.json` with a strict JSON parser (after a UTF-8 BOM), so setup reported `ready`, wrote a registration into a file the client rejects as corrupt, and doctor reported it `aligned`. Give Claude Code its own `claude_code` configuration format and parse it at the owning boundary with strict JSON.parse after removing a leading BOM. Setup, doctor, and uninstall all consume that parser, so comment or trailing-comma documents are now refused as malformed before any backup or write, while plain and BOM-prefixed JSON still configure. Clients that natively accept JSONC keep the `json` format and its behavior. Fixes #4940 Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>