Fix monotonic discovery path filters

[Widthdom]

Summary

• Make explicit --path filters intersect the implicit --exclude-tests production-source baseline.
• Apply the same composed scope to file rows, counts, generated exclusions, and repo maps.
• Expose effective include/exclude operators and provenance in JSON query context.
• Enforce the shared SQLite parameter budget across all composed path groups.

Validation

• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false --no-restore -m:1 -nodeReuse:false
• Focused Issue Make files path filters monotonic with implicit source and test exclusions #5229 tests on net8.0 and net9.0
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release -f net8.0 --no-build --no-restore -m:1 -nodeReuse:false (12,152 passed, 9 skipped)
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release -f net9.0 --no-build --no-restore -m:1 -nodeReuse:false (11,665 passed, 433 skipped)
• dotnet format CodeIndex.sln --verify-no-changes --no-restore --verbosity minimal
• dotnet run --project tools/CodeIndex.Changelog -- check
• Root index status --check and workspace status --check
• Codex adversarial review: No blocking/actionable issues found.

Documentation and changelog

• Updated USER_GUIDE.md in English and Japanese.
• Added changelog.d/unreleased/5229.fixed.md.

Follow-ups

• Stabilize C# regex allocation regression probes under full-suite load #5244

Fixes #5229