[codex] Add meaningful apply coverage tests

[satococoa]

What changed

• add integration tests for meaningful apply edge cases in the engine
• add CLI tests for quiet and verbose apply output behavior on the current main contract
• cover same-content skips, source symlink skips, and target-directory conflicts

Why

These cases represent real safety and UX expectations for ignored-file propagation between worktrees, and they were not covered before.

Impact

This raises confidence around apply behavior without adding coverage-only tests that lock in irrelevant implementation details.

Validation

• make test

[coderabbitai]

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/add-meaningful-coverage-tests

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