Fix Markdown dependency noise evidence

[Widthdom]

Summary

• classify dependency edges with provenance, reference kind, target kind, and reference-count evidence
• suppress legacy Markdown heading-name fanout without hiding explicit Markdown path links
• preserve structured symbol samples for comma-containing links and bound workspace-cycle candidate aggregation
• expose reference before/after totals and suppression reasons in JSON and JSON-graph output

Root cause and impact

Legacy Markdown heading references were ranked and filtered as ordinary symbol-name matches, so dense heading fanout could dominate dependency and cycle results. The dependency payload also flattened sampled symbols into a comma-delimited string, which made a valid comma-containing Markdown target ambiguous during later filtering and ranking.

The updated dependency pipeline distinguishes heading-derived evidence from explicit links, removes only the heading-derived counts, and keeps retained evidence ahead of candidate limits. Workspace-cycle aggregation now keeps bounded retained/suppressed buckets instead of accumulating every database-pair result.

Validation

• dotnet format CodeIndex.sln --verify-no-changes --no-restore
• dotnet build CodeIndex.sln -c Release --no-restore — 0 warnings, 0 errors
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release --no-build --filter Issue4868 — 6 passed on both .NET 8 and .NET 9
• relevant dependency/JSON regression filter — 92 passed on .NET 8; 91 passed and 1 known performance-test skip on .NET 9
• broad DbReaderTests / RunDeps regression filter — 700 passed on .NET 8; 699 passed and 1 known performance-test skip on .NET 9
• dotnet run --project tools/CodeIndex.Changelog -- check — 38 fragments validated
• local cdidx status --check --json — index_matches_workspace: true
• Codex adversarial review completed in two rounds; all actionable findings were addressed

Documentation and changelog

Updated the English and Japanese dependency contracts in README.md, USER_GUIDE.md, and DEVELOPER_GUIDE.md.

Changelog fragment: changelog.d/unreleased/4868.fixed.md

Follow-ups

None identified within this issue scope.

Fixes #4868