Fix filtered portable archive trust metadata

[Widthdom]

Summary

• mark filtered portable archives and conservative legacy imports incomplete with the stable partial_archive reason and explicit whole-source scope
• remove source-wide HEAD/run provenance and omit unavailable unknown-extension coverage while preserving the source database and full unfiltered archives
• require a full workspace scan before a later scoped index can clear partial-archive trust
• release the scoped archive test database connection before hashing so Windows does not retain a conflicting SQLite file handle

Validation

• merged latest origin/main at fd3c30312
• dotnet build CodeIndex.sln -c Release --no-restore (0 warnings, 0 errors)
• dotnet format CodeIndex.sln --verify-no-changes --no-restore
• dotnet run --project tools/CodeIndex.Changelog -- check (3 fragments after the main merge)
• ExportImportCommandRunnerTests in Release: 68/68 passed on .NET 8 and 68/68 passed on .NET 9
• targeted filtered-archive/full-scan regression: passed on .NET 8 and .NET 9
• existing Preserve committed graph data and report truthful state after per-file extraction failures #4609 incomplete-index regression: passed on .NET 8 and .NET 9
• full Release .NET 9 suite during implementation: 10,716 passed, 412 skipped, 0 failed
• local full index refresh and status --check: fresh and complete

Adversarial review

• Round 1: fixed both findings covering legacy databases without codeindex_meta and import JSON/DB incomplete-reason alignment.
• Round 2: fixed both findings covering scoped updates after partial imports and non-authoritative unknown-extension zero values.
• The repository workflow caps the adversarial review loop at two rounds; every finding from both rounds is addressed and covered by focused regression tests.

Documentation and changelog

• Updated the English and Japanese sections of USER_GUIDE.md, DEVELOPER_GUIDE.md, and TESTING_GUIDE.md.
• Added bilingual fragment changelog.d/unreleased/5053.fixed.md.

Fixes #5053