Fix report manifests, metadata targets, and git diagnostics

[Widthdom]

Summary

• Add a support manifest to report bundles with redaction, omission, readiness, and diagnostic summaries.
• Persist C# metadata target provenance and use source-aware readiness/diff behavior.
• Return structured, bounded git process failures and propagate root-discovery failures.

Tests

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~ReportCommandRunnerTests|FullyQualifiedName~GitHelperTests|FullyQualifiedName~DiffCommandRunnerTests|FullyQualifiedName~Issue3524" -p:UseSharedCompilation=false
• dotnet build CodeIndex.sln -p:UseSharedCompilation=false
• dotnet run --project tools/CodeIndex.Changelog -- check
• git diff --check origin/main..HEAD
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll index . --json
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json

Fixes #3555
Fixes #3524
Fixes #3434

[Widthdom]

Superseded by #3633 after origin/main advanced during finalization. Closing this duplicate PR.