The step_register_skills_table step called add_skill in a loop but only
committed once at the end. Because SkillRepository.create() obtains a
new session per call and only flushes (never commits), the intermediate
sessions could be garbage-collected before the final commit, rolling
back their transactions on the shared SQLite :memory: connection. Moving
_commit_pending inside the loop ensures each skill is durably committed
before the next session is created.
ISSUES CLOSED: #418
