Fix logical partial-family impact traversal

[Widthdom]

Summary

• Treat one current C# logical partial family as a single impact traversal root while querying the union of its bounded physical symbol identities and definition paths.
• Deduplicate callers, file hints, cycles, and converging shortest paths across family members while retaining representative and physical-member evidence.
• Preserve physical multi-file ambiguity on stale reference-identity indexes, keep unrelated same-name symbols ambiguous, and expose family-root scope, limits, omissions, and count authority in CLI/MCP output.

Validation

• dotnet build CodeIndex.sln --configuration Release: passed with 0 warnings and 0 errors, including after merging the latest origin/main.
• Full Release solution tests: .NET 8 passed 11,241 with 7 skipped; .NET 9 passed 10,774 with 413 skipped; 0 failures.
• Broad impact-focused tests after review fixes: 108 passed on both .NET 8 and .NET 9.
• Post-origin/main merge impact tests: 125 passed on both .NET 8 and .NET 9.
• Final stale-identity regression test: passed on both .NET 8 and .NET 9.
• dotnet format CodeIndex.sln --verify-no-changes --no-restore: passed.
• dotnet run --project tools/CodeIndex.Changelog -- check: validated all 9 current fragments after the latest origin/main merge.
• git diff --check: passed.
• Repository-scale reproduction for impact QueryCommandRunner --max-hops 4 --json --limit 50 --count: returned 10 results across 10 files from a 64-member logical family without truncation.
• Mandatory Codex adversarial review completed in 2 rounds; all actionable findings from both rounds were fixed and covered by regressions.

Documentation and changelog

• Updated the English and Japanese sections of USER_GUIDE.md, DEVELOPER_GUIDE.md, and TESTING_GUIDE.md.
• Added changelog.d/unreleased/5060.fixed.md.

Follow-up candidates

• None.

Fixes #5060