Clarify status readiness degradation signals

[Widthdom]

Summary

• Add structured status readiness degradation guidance with top-level root cause and per-field readiness_degradations.
• Split physical file_issues table presence from current file issue data via file_issues_data_current.
• Surface migration/write-in-progress readiness state in status output.

Validation

• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release -p:UseSharedCompilation=false --filter "FullyQualifiedNameQueryCommandRunnerTests.RunStatus_HumanOutput_TranslatesReadinessFields|FullyQualifiedNameQueryCommandRunnerTests.RunStatus_CheckJsonScopedReadiness_ReportsOnlyRequestedSubsystem|FullyQualifiedNameJsonOutputSnapshotTests.RunStatus_JsonOutput_MatchesGolden|FullyQualifiedNameLegacySchemaMigrationTests|FullyQualifiedNameDocumentationStatusContractTests|FullyQualifiedNameQueryCommandRunnerTests.RunStatus_Json_ReportsStructuredGuidanceForMultipleReadinessDegradations"
• env GIT_CONFIG_COUNT=1 GIT_CONFIG_KEY_0=commit.gpgsign GIT_CONFIG_VALUE_0=false dotnet test CodeIndex.sln -c Release -p:UseSharedCompilation=false (net9 passed; net8 had one GlobalToolLogTests flake that passed when rerun alone)
• targeted cdidx index update for changed files

Documentation / Changelog

• Updated README.md, AGENT_GUIDE.md, and DEVELOPER_GUIDE.md status contract documentation.
• Added changelog fragment: changelog.d/unreleased/1484.fixed.md

Follow-up

• index: full scan stalls extracting SqlReferenceExtractor.cs symbols #2710 tracks the unrelated full-index refresh stall encountered while following the repository indexing workflow.

Fixes #1931
Fixes #1484
Fixes #1486
Fixes #1761