fix(detect-custom-files): add skills/ to GSD_MANAGED_DIRS (#2942) (#2945)

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>

get-shit-done/bin/gsd-tools.cjs

@@ -1070,6 +1070,7 @@ async function runCommand(command, args, cwd, raw, defaultValue) {
         'agents',
         path.join('commands', 'gsd'),
         'hooks',
+        'skills',
       ];
 
       function walkDir(dir, baseDir) {