Fix no-op status freshness consistency

[Widthdom]

Summary

• centralize ordinary, checked, workspace, and MCP status freshness classification for checksum-reused no-op updates
• require trustworthy HEAD, worktree, timestamp, and Git-index evidence before ordinary status reports fresh
• force untracked-file visibility, report dirty ordinary status as explicitly unknown, and let an authoritative matching check prove already-indexed untracked paths fresh
• propagate same-commit branch drift into checked failures, exit status, and workspace member health
• gate the repository-wide Git-index visibility scan behind all ordinary-status trust preconditions
• stabilize the CI performance smoke budget by explicitly distinguishing coverage-instrumented runs from ordinary retries
• add deterministic unit, integration, matrix, CLI, workspace, MCP, and CI regression coverage

Validation

• dotnet build CodeIndex.sln -c Release --no-restore -p:UseSharedCompilation=false
• post-main-merge targeted Issue Make ordinary status honor no-op workspace freshening consistently with --check #5227 and CI regression tests: .NET 8: 93 passed; .NET 9: 93 passed
• coverage-instrumented performance smoke invocation: passed
• non-coverage focused performance smoke invocation: passed
• full .NET 8 suite: 12,131 passed, 9 skipped, 0 failed
• full .NET 9 suite: 11,645 passed, 432 skipped, 0 failed
• dotnet format CodeIndex.sln --no-restore --verify-no-changes
• make lint
• dotnet run --project tools/CodeIndex.Changelog -- check
• git diff --check and git diff --cached --check
• local root index refresh completed successfully
• Codex adversarial review: two post-pipeline rounds completed; all five actionable findings were remediated and regression-tested

Documentation and changelog

• updated the English and Japanese sections of README.md, DEVELOPER_GUIDE.md, and TESTING_GUIDE.md
• updated changelog.d/unreleased/5227.fixed.md

Follow-ups

• None.

Collaborator checklist

• The change follows the existing code style.
• The change includes tests when behavior changes.
• The change includes a changelog fragment when user-visible behavior changes.
• Documentation has been updated when needed.

Fixes #5227
Fixes #5243