Classify validate replacement characters

[Widthdom]

Summary

• Add origin/severity metadata to validate replacement_char diagnostics.
• Classify intentional U+FFFD literals as source_literal/info and decoder replacements as decode_replacement/warning.
• Preserve new file_issues metadata through DB reads, writes, migrations, and unchanged-file reuse.

Validation

• dotnet build
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedNameValidateContent_|FullyQualifiedNameRunValidate_ReplacementCharJson_IncludesOriginAndSeverity|FullyQualifiedName~GetUnchangedFileId_ReturnsNullWhen"
• dotnet run --project tools/CodeIndex.Changelog -- check
• cdidx status --check --json
• cdidx validate --json

Notes

• Full dotnet test exposed unrelated flaky reference extraction failures; tracked in Flaky full dotnet test run can fail reference extraction tests #2945.
• Adversarial review: No blocking/actionable issues found.

Fixes #2814