Previously, SetupRedirect used os.RemoveAll() which deleted all files in .beads/ including tracked files like formulas/, README.md, config.yaml. Now cleanBeadsRuntimeFiles() selectively removes only gitignored runtime files (*.db, daemon.*, issues.jsonl, etc.) while preserving tracked content. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>