fix(checkpoints): block primary checkout capture and preserve run finalization

[Mjones13]

Primary Git checkout capture can retain unrelated files in hidden checkpoint refs. Reject it with a typed error before index/object/ref writers; linked worktrees retain capture and restoration behavior. This ports owner PR #10 onto the pinned nightly rebuild and current staging ancestry.

• Preserves all existing checkpoint assertions, moves capture fixtures into disposable linked worktrees, and adds clean/dirty primary and metadata-only no-writer regressions.
• Verifies that a local-mode run completes with checkpoint status error when the real checkpoint services receive the typed refusal. The store boundary is synthetic in this service test; physical Git refusal is tested separately.
• Repairs an existing review-preview fixture to set disk executable mode as well as index mode, preserving every rename/path/mode/binary assertion and production preview behavior.

Validation: 198 tests passed across the five affected modules with no skips; server and contract types passed; formatting and scoped lint passed (one unchanged schema-compilation warning). The two primary-refusal cases failed as expected against the parent writer. Final head integrates staging with a normal merge. No live runtime adoption or provider-session qualification performed.

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