docs: clarify node_modules guidance
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## Agent-Specific Notes
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- Vocabulary: "makeup" = "mac app".
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- Never edit `node_modules` (global/Homebrew/npm/git installs too). Updates overwrite. Skill notes go in `tools.md` or `AGENTS.md`.
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- When working on a GitHub Issue or PR, print the full URL at the end of the task.
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- When answering questions, respond with high-confidence answers only: verify in code; do not guess.
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- Never update the Carbon dependency.
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