Fixes from maphew including:
- Remove test for deleted isPathWithinDir function
- Add gosec nolint directives for safe file operations
- Add rm -rf .beads before init in CI workflow
- Simplify panic handling and file operations
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Co-Authored-By: maphew <maphew@users.noreply.github.com>
Co-Authored-By: Claude <noreply@anthropic.com>