Add scientific and native-extension reference graphs

[Widthdom]

Summary

• add bounded symbol and reference graph extraction for Nim, MATLAB, Julia, D, Cython, Ada, and ambiguous .m files
• preserve language-specific identity, qualified target resolution, scoping, and comment/string masking across indexing, persisted lookup, hook mutation, and fold backfill paths
• document the supported graph contracts in the English and Japanese guide sections and add changelog.d/unreleased/4738.added.md

Why

These languages were recognized by CodeIndex but did not have complete reference-graph contracts, so calls, imports, type relationships, and module relationships were unavailable or inconsistently resolved. This change adds deterministic, bounded extraction and persistence behavior while keeping ambiguous .m handling safe across MATLAB and Objective-C syntax.

User impact

references, callers, callees, impact, and related graph queries can now follow supported relationships in these scientific and native-extension languages. Nim identifier identity, Julia index sentinels, D receivers, Ada ranges and forward declarations, and ambiguous .m classification retain their language-specific semantics.

Validation

• dotnet build CodeIndex.sln -c Release --no-restore -p:UseSharedCompilation=false
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release --no-build --no-restore -f net8.0 -p:UseSharedCompilation=false --filter "FullyQualifiedName~Issue4738" — 132 passed
• equivalent net9.0 Add reference graphs for scientific and native-extension languages #4738 run — 132 passed
• full Release solution suite — net8.0: 10,356 passed / 7 skipped; net9.0: 9,897 passed / 404 skipped with one unrelated ConsoleCapture parallel flake that passed in isolation (Full-suite ConsoleCapture test can race with parallel console mutation #4800)
• merged CLI and Add reference graphs for scientific and native-extension languages #4738 net9.0 group — 735 passed / 84 skipped; the corresponding net8.0 group had one unrelated installer-cancellation flake that passed in isolation (Installer cancellation test can parse an empty PID file under load #4801)
• make lint
• dotnet format CodeIndex.sln --no-restore --verify-no-changes --verbosity minimal
• dotnet run --project tools/CodeIndex.Changelog -- check
• post-commit Debug rebuild, workspace re-index, and status --check --json
• two codex review --base origin/main adversarial-review rounds; all actionable findings addressed and regression-tested

Follow-ups

• Full-suite ConsoleCapture test can race with parallel console mutation #4800
• Installer cancellation test can parse an empty PID file under load #4801

Fixes #4738