Replace directory symlinks (gstack/qa → qa) with real directories
containing a SKILL.md symlink. Claude Code auto-prefixes skills nested
under a parent dir symlink, so /plan-ceo-review became "Unknown skill"
even with skill_prefix=false. Real dirs fix this.
Also syncs package.json version to match VERSION file and updates
test assertions to match the new mkdir + ln approach.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>