Stabilize bounded regex extraction under load

[Widthdom]

Summary

• Increase the bounded regex default timeout to the same 2s budget used by runtime safety so reference extraction does not fail closed under grouped/full-suite load.
• Add a regression guard that keeps the bounded regex timeout and runtime safety timeout aligned.
• Add changelog fragments for QueryCommandRunner SQL reference JSON test is flaky under grouped net9 runs #2943 and Flaky full dotnet test run can fail reference extraction tests #2945.

Validation

• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~ReferenceExtractorTests.Extract_FSharp_DetectsWhenGuardApplicationCalls|FullyQualifiedName~QueryCommandRunnerTests.RunReferences_ExactJson_SqlTruncateTargetsHandleOnlyAndMultipleTargets|FullyQualifiedName~QueryCommandRunnerTests.RunReferences_ExactJson_SqlLineEndCommentsKeepUnfinishedTargetPrefixes|FullyQualifiedName~QueryCommandRunnerTests.RunReferences_ExactJson_SqlMergeTempTargetWithMultilineHintResolvesTargetAndSource|FullyQualifiedName~BoundedRegexTests.DefaultMatchTimeout_MatchesRuntimeSafetyTimeout"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release --framework net9.0 --filter "FullyQualifiedName~ExportImportCommandRunnerTests|FullyQualifiedName~ReportCommandRunnerTests|FullyQualifiedName~QueryCommandRunnerTests.RunReferences_ExactJson_SqlMergeTempTargetWithMultilineHintResolvesTargetAndSource|FullyQualifiedName~QueryCommandRunnerTests.RunReferences_ExactJson_SqlUsingSourceMatcherSkipsDdlUsingClauses"
• git diff --check
• dotnet build
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• Codex adversarial review: no blocking/actionable issues found.

Notes

• No AGENT.md, CLAUDE.md, or AGENT_GUIDE.md changes.
• No additional follow-up issues were identified.

Fixes #2943
Fixes #2945