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The Permission Manager skill simplifies the setup of Claude Code by managing the .claude/settings.json file specifically for repository-centric workflows. It eliminates repetitive permission prompts by pre-authorizing safe Git and GitHub CLI (gh) commands, while maintaining a strict security layer that blocks high-risk operations like destructive file deletions or force-pushing to production branches. By providing a detailed delta analysis and requiring explicit user confirmation for all changes, it ensures developers maintain full control over their environment's security posture.