fix: resolve bash tool path validation relative to cwd

[riatzukiza]

Summary

• resolve the requested working directory relative to the project root when using realpath
• validate destructive command arguments using the effective working directory so relative parent paths inside the project are accepted

Testing

• not run

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https://chatgpt.com/codex/tasks/task_e_6903d154f9888324bfbfd8b138b07833

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✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch codex/fix-cwd-validation-for-command-paths

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