After v1.39.0 skill consolidation (#2790), skills/ became a GSD-managed root that the installer wipes on update. GSD_MANAGED_DIRS in gsd-tools.cjs was missing 'skills', so user-added skill directories (e.g. skills/custom-skill/SKILL.md) were never walked and silently destroyed during /gsd-update. - Add 'skills' to GSD_MANAGED_DIRS so the directory is walked - Add tests/bug-2942-detect-custom-skills.test.cjs with 5 targeted tests - Update tests/update-custom-backup.test.cjs: replace the now-incorrect "skills/ must NOT be scanned" assertion (written pre-#2790) with a test that verifies custom skills ARE detected and GSD-owned skills are not falsely flagged Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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