feat(enable): restore the checkpoint-storage question, git-refs recommended

Team decision on the removed wizard question (#1789): keep it, but flip the recommendation — git-refs listed first, pre-selected, labeled '(recommended)' instead of branch being 'the default'. One Enter accepts refs; the choice is written explicitly either way. Non-interactive, --yes, and cancelled first runs take the recommendation silently, and the prompt is skipped while ENTIRE_CHECKPOINTS_PRIMARY is active (an answer could not take effect and would only write diverging config). Existing repos remain untouched.