Make export and report outputs atomic

[Widthdom]

Summary

• Stage cdidx export archives, cdidx export ctags tagfiles, and cdidx report bundles in same-directory temporary files before replacing requested outputs.
• Replace imported databases before deleting destination SQLite WAL/SHM sidecars.
• Add regression tests for preserving existing outputs and sidecars when replacement fails.

Validation

• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release --filter "FullyQualifiedName~ExportImportCommandRunnerTests|FullyQualifiedName~ReportCommandRunnerTests" -p:UseSharedCompilation=false
• dotnet format CodeIndex.sln --verify-no-changes
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json

Documentation And Changelog

• Added bilingual changelog fragments:
  • changelog.d/unreleased/2839.fixed.md
  • changelog.d/unreleased/2842.fixed.md
  • changelog.d/unreleased/2850.fixed.md
  • changelog.d/unreleased/2886.fixed.md

Follow-Up References

• QueryCommandRunner SQL reference JSON test is flaky under grouped net9 runs #2943

Fixes #2839
Fixes #2842
Fixes #2886
Fixes #2850