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init\n```\n\nRemove pre-commit hook:\n\n```bash\nathena uninstall\n```\n\nSetup scanner dependencies:\n\n```bash\nathena setup all\nathena setup all --auto\nathena setup semgrep\nathena setup semgrep --auto\nathena doctor --fix\n```\n\n## Common Options\n\nSet threshold (default is `9`):\n\n```bash\nathena scan . --threshold 9\nathena check --threshold 9\n```\n\nChoose output format:\n\n```bash\nathena scan . --format terminal\nathena scan . --format json\nathena scan . --format jsonl\n```\n\n## Terminal UI Behavior\n\n- Selector mode renders in-place and re-renders dynamically.\n- Scan/check reports separate AI-origin confidence from security findings.\n- Direct command runs clear the terminal before rendering report output.\n\n## Report Highlights\n\nTerminal reports include:\n\n- Top-level metrics (`files`, `units`, `ai-flagged units`, `duration`)\n- AI-origin confidence section\n- Top weighted signals\n- Security findings section\n- Gate status and gate reason\n\n## Development\n\nRun from source:\n\n```bash\nnpm run dev -w @arsh342/athena -- menu\n```\n\nQuiet npm wrapper output:\n\n```bash\nnpm run -s dev -w @arsh342/athena -- menu\n```\n\nBuild:\n\n```bash\nnpm run build -w @arsh342/athena\n```\n\n## Notes\n\n- Runs fully local (no external AI service required).\n- Supports JavaScript, TypeScript, JSX, and TSX.\n- Requires Node.js 18 or newer.\n- ESLint scanner support is bundled through Athena optional package dependencies.\n- Semgrep, Docker (for nodejsscan), and Bearer CLI remain external optional tools.\n","readmeFilename":"README.md"}