Tibsfox 88af6fdcda fix(reapply-patches): three-way merge and never-skip invariant for backed-up files ...

The reapply-patches workflow used a two-way comparison (user's backup vs
new version) which couldn't distinguish user customizations from version
drift. This caused 10/10 files to be misclassified as "no custom content"
in real-world usage, silently discarding user modifications.

Changes:
- Rewrite workflow with three-way merge strategy (pristine baseline vs
  user-modified backup vs newly installed version)
- Add critical invariant: files in gsd-local-patches/ must NEVER be
  classified as "no custom content" — they were backed up because the
  installer's hash check detected modifications
- Add git-aware detection path using commit history when config dir is
  a git repo
- Add pristine_hashes to backup-meta.json so the reapply workflow can
  verify reconstructed baseline files
- Add from_manifest_timestamp to backup-meta.json for version tracking
- Conservative default: flag as CONFLICT when uncertain, not SKIP

Closes #1469

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

2026-03-29 10:04:22 -07:00

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