Report persisted index completeness consistently

[Widthdom]

Summary

• derive index and reference-graph completeness from one persisted readiness snapshot across indexing output, status, workspace health, and MCP
• preserve omission reasons for file-size, symbol, reference, extraction, and symbols-only cases, including policy changes on otherwise unchanged files
• expose stable structured reason arrays and remediation while avoiding fold-only guidance for an incomplete generation

Validation

• dotnet restore CodeIndex.sln
• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false (0 warnings, 0 errors)
• full Release suite before review fixes:
  • .NET 8: 10,479 passed, 7 skipped, 0 failed
  • .NET 9: 10,006 passed, 419 skipped, 0 failed
• post-review Issue Report index and graph completeness truthfully for capped and symbols-only builds #4826 tests:
  • .NET 8: 12 passed
  • .NET 9: 12 passed
• post-review readiness/stat-reuse regression tests:
  • .NET 8 Release: 24 passed
  • .NET 9 Release: 24 passed
• dotnet format CodeIndex.sln --verify-no-changes --no-restore --verbosity minimal
• dotnet run --project tools/CodeIndex.Changelog -- check
• git diff --check

Documentation and changelog

• updated the English and Japanese contracts in README.md, DEVELOPER_GUIDE.md, and TESTING_GUIDE.md
• clarified the persisted readiness status contract in AGENT_GUIDE.md
• added changelog.d/unreleased/4826.fixed.md

Adversarial review

• completed the workflow maximum of two Codex adversarial-review rounds
• addressed every actionable finding with regression coverage for scoped update evidence, symbols-only remediation, file-size policy transitions, and incomplete-generation guidance

Follow-up candidates

None.

Fixes #4826