feat(enable): default new setups to the git-refs checkpoint backend

Drop the Branch-vs-Refs wizard question — a storage-topology choice is unanswerable during first-time setup — and instead write checkpoints.primary.type: git-refs explicitly into the new settings.json on every first run (interactive wizard and --agent alike). One less setup step.

Nothing else moves:

• --checkpoint-backend branch still wins over the default; its help text now names refs as the new-setup default.
• The config-less runtime fallback stays git-branch, so repos set up before this change keep their behavior; re-running enable on such a repo does not inject a checkpoints block (pinned by test).
• Switching later stays one command (entire configure --checkpoint-backend), read routing keeps both formats readable, and doctor migrate-checkpoints still converts history outright.