Fix index refresh stalls on large C# files

[Widthdom]

Summary

• Batch upsert reference_lines during reference insertion instead of doing one INSERT ... RETURNING per unique line.
• Refresh mutual-recursion flags through folded-name columns backed by a dedicated index.
• Reuse already sanitized C# match lines while resolving brace ranges.

Validation

• dotnet build src/CodeIndex/CodeIndex.csproj -p:UseSharedCompilation=false
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release -p:UseSharedCompilation=false --filter "FullyQualifiedName~DatabaseTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release -p:UseSharedCompilation=false --filter "FullyQualifiedName~SymbolExtractorTests"
• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet test CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll index . --files tests/CodeIndex.Tests/QueryCommandRunnerTests.cs --db /private/tmp/cdidx-2528-clean.db --json
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll . --json
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• git diff --cached --check
• Codex adversarial review: no blocking/actionable issues found.

Documentation / Changelog

• Added changelog.d/unreleased/2528.fixed.md.

Follow-up Candidates

• None.

Fixes #2528