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>
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