Fix query freshness accounting for zero matches

[Widthdom]

Summary

• Separate query result cardinality from freshness so clean zero-match named and recipe queries are not reported as stale.
• Derive freshness from workspace/index state, recipe/query definition versions, and child execution validity.
• Keep structured freshness aligned across aggregate/compact/count JSON, text, SARIF, and issue-draft output, including classified child failures.
• Verify Git and non-Git workspaces while avoiding workspace scans for text-only named counts.

Root cause

zero_result_query_count was also used to populate stale_query_names, so a valid zero-result execution was treated as freshness invalidation. The previous execution path also lacked persistent definition identities and structured failed-child observations.

Validation

• dotnet build CodeIndex.sln -c Release --no-restore -p:UseSharedCompilation=false — passed with 0 warnings and 0 errors.
• Focused Issue Represent clean named queries separately from stale queries #4907 / SARIF integration tests: 11/11 passed on net8.0 and 11/11 passed on net9.0.
• CI-regression freshness fixtures: 5/5 passed on net8.0 and 5/5 passed on net9.0.
• Latest-main Make safety audits understand safe helper and negative-policy semantics #4911/Let safety audits use guard evidence beyond a narrow local window #4912 integration tests: 9/9 passed on net8.0.
• Full net8.0 suite: 11,049 passed, 7 skipped; one unrelated Avoid overhead that makes parallel batch slower than sequential #4872 parallel timing test timed out under full-suite load and passed 1/1 when rerun alone.
• Full net9.0 suite: 10,576 passed, 420 skipped, 0 failed.
• dotnet run --project tools/CodeIndex.Changelog -- check — validated 90 fragments.
• Local index freshness check — 1,327/1,327 files matched, failed_checks: [].
• Two adversarial-review rounds completed; all actionable findings were addressed.

Documentation and changelog

• Updated the English and Japanese query-freshness sections in USER_GUIDE.md and TESTING_GUIDE.md.
• Added changelog.d/unreleased/4907.fixed.md.

Follow-ups

None.

Fixes #4907