Make large dependency cycles actionable (#5197)

[Widthdom]

Summary

• Keep dependency-cycle SCC analysis authoritative while bounding default node materialization to 50 nodes per component across CLI and MCP output formats.
• Add compact summaries, complete omission/evidence metadata, stable evidence-bound cursors, and bounded JSON graph projections.
• Suppress only non-authoritative qualified C# call edges, including same-name files outside resolved-group candidate sets, while preserving confirmed targets and failing closed for stale identity contracts.

Validation

• dotnet test CodeIndex.sln -c Release -p:UseSharedCompilation=false -m:1 --no-build --no-restore
  • net8.0: 12,056 passed, 9 skipped, 0 failed
  • net9.0: 11,571 passed, 431 skipped, 0 failed
• Issue Make large dependency SCCs bounded and actionable #5197 focused Release tests: 12 passed on each TFM.
• Broader dependency-query adversarial-review tests: 114 total on each TFM, with 1 expected net9.0 skip.
• Changelog fragment validation: 16 fragments validated.
• Repository and workspace index checks are healthy and match the worktree.
• Mandatory Codex adversarial review completed with no blocking or actionable correctness issues.

Documentation and changelog

• Updated the English and Japanese dependency-cycle documentation in USER_GUIDE.md, DEVELOPER_GUIDE.md, and TESTING_GUIDE.md.
• Added changelog.d/unreleased/5197.changed.md.

Follow-ups

None.

Fixes #5197