Fix noisy dependency and hotspot rankings

[Widthdom]

Summary

• Rank deps and hotspots --group-by file by noise-adjusted ranking_score while preserving raw reference_count.
• Add JSON diagnostics for dependency/file-hotspot ranking scores and penalties.
• Add regression coverage for noisy dependency edges and tiny high-count hotspot files.

Validation

• dotnet build src/CodeIndex/CodeIndex.csproj --no-restore -p:UseSharedCompilation=false -p:BuildInParallel=false -m:1
• dotnet build tests/CodeIndex.Tests/CodeIndex.Tests.csproj --framework net8.0 --no-restore -p:UseSharedCompilation=false -p:BuildInParallel=false -m:1
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --no-build --framework net8.0 --filter "FullyQualifiedName~GetFileDependencies_RanksNoiseAdjustedEdgesBeforeApplyingLimit_Issue4113|FullyQualifiedName~GetFileSymbolHotspots_RanksBroadFilesAheadOfTinyHighCountFiles_Issue4113|FullyQualifiedName~RunDeps_JsonFiltersNoiseSymbolsAndAddsMetadata_Issue3943|FullyQualifiedName~RunDeps_JsonGraph_WritesValidGraphPayload"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --framework net9.0 --no-restore --filter "FullyQualifiedName~GetFileDependencies_RanksNoiseAdjustedEdgesBeforeApplyingLimit_Issue4113|FullyQualifiedName~GetFileSymbolHotspots_RanksBroadFilesAheadOfTinyHighCountFiles_Issue4113|FullyQualifiedName~RunDeps_JsonFiltersNoiseSymbolsAndAddsMetadata_Issue3943|FullyQualifiedName~RunDeps_JsonGraph_WritesValidGraphPayload" -p:UseSharedCompilation=false -p:BuildInParallel=false -m:1
• dotnet format CodeIndex.sln --verify-no-changes --no-restore --include src/CodeIndex/Cli/QueryCommandRunner.cs src/CodeIndex/Cli/QueryCommandRunner.Hotspots.cs src/CodeIndex/Database/DbReader.Dependencies.cs src/CodeIndex/Database/DbReader.GraphQueries.cs src/CodeIndex/Database/DbSymbolReader.cs src/CodeIndex/Mcp/McpToolHandlers.cs src/CodeIndex/Models/QueryResults.cs src/CodeIndex/Models/DependencyNoiseProfile.cs tests/CodeIndex.Tests/DbReaderFileDependencyTests.cs tests/CodeIndex.Tests/DbReaderTests.cs tests/CodeIndex.Tests/QueryCommandRunnerTests.cs
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll deps --format edgelist --limit 20 --exclude-tests
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll hotspots --group-by file --exclude-tests --limit 20

Documentation and changelog

• Updated USER_GUIDE.md.
• Added changelog.d/unreleased/4113.fixed.md.

Follow-up candidates

• None.

Fixes #4113