Spec Kitty

Mission Run: Schema-3 upgrade commits only what it changed

Stop spec-kitty upgrade from sweeping a project's uncommitted work, including untracked secrets, into the schema-3 migration commit and from bypassing commit hooks (#5443).

Upgrading a 2.x project runs a migration that commits with git add -A and retries with --no-verify, so untracked secrets, staged files and unrelated edits are committed at exit 0 and a hook that would have refused them is skipped. This mission routes the migration's changes through the upgrade command's existing commit, which only commits paths the upgrade changed and honours hooks.