The cleanup-legacy.py script used an overly broad rglob("SKILL.md") that
matched template and asset files nested deep in the directory tree (e.g.
bmad-module-builder/assets/setup-skill-template/SKILL.md). This caused
cleanup to abort when it couldn't verify non-installable templates at the
skills directory.
Scopes find_skill_dirs() to only match SKILL.md at recognized installable
positions: direct children ({name}/SKILL.md) and skills subfolder
(skills/{name}/SKILL.md). Also adds config.yaml backup/restore around
shutil.rmtree() so per-module configs needed by bmad-init are preserved.
Fixes#2175
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
DJ