Ryan a11b20960a fix(doctor): UX improvements for diagnostics and daemon (#687) ...

* fix(doctor): UX improvements for diagnostics and daemon

- Add Repo Fingerprint check to detect when database belongs to a
  different repository (copied .beads dir or git remote URL change)
- Add interactive fix for repo fingerprint with options: update repo ID,
  reinitialize database, or skip
- Add visible warning when daemon takes >5s to start, recommending
  'bd doctor' for diagnosis
- Detect install method (Homebrew vs script) and show only relevant
  upgrade command
- Improve WARNINGS section:
  - Add icons (⚠ or ✖) next to each item
  - Color numbers by severity (yellow for warnings, red for errors)
  - Render entire error lines in red
  - Sort by severity (errors first)
  - Fix alignment with checkmarks above
- Use heavier fail icon (✖) for better visibility
- Add integration and validation tests for doctor fixes

* fix(lint): address errcheck and gosec warnings

- mol_bond.go: explicitly ignore ephStore.Close() error
- beads.go: add nosec for .gitignore file permissions (0644 is standard)

2025-12-22 01:25:23 -08:00

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