Switching writes to new ref store

[Soph]

https://entire.io/gh/entireio/cli/trails/767

Let's enable the new ref backend. All new writes will go there, all reads go to where the checkpoint is (easy check by different checkpoint format)

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Note

Medium Risk
Changes where and how new checkpoints are persisted for anyone using this settings file; existing hex/git-branch checkpoints should still read via ID routing, but mixed backends increase operational surface during the migration.

Overview
Turns on the git-refs primary checkpoint backend for this repo’s checked-in Entire local settings by adding checkpoints.primary.type: "git-refs". With that primary, new checkpoint writes go to the per-checkpoint git-ref store (ULID IDs) instead of the default git-branch / v1 layout; reads continue to resolve the correct backend from each checkpoint’s ID shape.

Also fixes JSON formatting (trailing comma after strategy) in the same file.

^{Reviewed by Cursor Bugbot for commit 74b8eea. Configure here.}

[Copilot]

Pull request overview

This PR flips the repository’s default checkpoint backend configuration so new checkpoint writes use the git-refs store, aligning local/dev behavior with the newer per-checkpoint ref backend while keeping read behavior format-routed by checkpoint ID kind.

Changes:

• Update .entire/settings.json to set checkpoints.primary.type to git-refs.
• Adjust JSON formatting to accommodate the new checkpoints block.