Fix workspace baseline branch safety

[christso]

Summary

• Use private shadow refs for dirty existing Git workspace baselines instead of committing to user branch.
• Keep clean existing workspaces returning existing HEAD as baseline.
• Capture file changes with temporary indices to avoid user index mutation.
• Preserve nested git repo diffs while restoring nested index state after capture.

Verification

• bun test packages/core/test/evaluation/workspace/file-changes.test.ts
• bun --filter @agentv/core typecheck (fails in this environment: tsc not available in PATH)
• Dogfood evidence: /home/entity/projects/EntityProcess/agentv-private/dogfood-av-cuf-2026-06-26.txt

[cloudflare-workers-and-pages]

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