Add status diagnostics and maintenance guidance

[Widthdom]

Summary

• Classify status --json unknown-extension output into extension counts, category counts, and grouped recommendations.
• Add stable severity, diagnostic code, and object-count metadata to DB diagnostic JSON output.
• Add WAL/freelist maintenance guidance to status and vacuum output, including vacuum --dry-run.
• Expose structured status --check --json repair commands and last failed/partial index-run context.

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~IndexCommandRunnerTests.Run_VerboseReportsUnknownExtensionCountAndStatusJsonStampsCount|FullyQualifiedName~DocumentationStatusContractTests|FullyQualifiedName~DbCommandRunnerTests.RunIntegrityCheck_JsonIncludesStableSeverityAndDiagnosticCode_Issue3565|FullyQualifiedName~DbCommandRunnerTests.RunSchema_JsonIncludesSeverityAndObjectCounts_Issue3565|FullyQualifiedName~DbCommandRunnerTests.RunSchema_JsonReportsOmittedObjectCountsWhenTruncated_Issue3565|FullyQualifiedName~DatabaseTests.RunIncrementalVacuum_DryRunReportsEstimateWithoutChangingFreelist_Issue3564|FullyQualifiedName~QueryCommandRunnerTests.RunStatus_JsonIncludesMaintenanceGuidance_Issue3564|FullyQualifiedName~QueryCommandRunnerTests.RunVacuum_DryRunJsonReportsMaintenanceGuidance_Issue3564|FullyQualifiedName~QueryCommandRunnerTests.RunStatus_CheckJson_ReportsRepairCommandsForWorkspaceStale_Issue3567|FullyQualifiedName~QueryCommandRunnerTests.RunStatus_CheckJson_OmitsRepairCommandsWhenHealthy_Issue3567|FullyQualifiedName~QueryCommandRunnerTests.RunStatus_CheckJson_ReportsBackfillRepairCommandForFoldDegradation_Issue3567|FullyQualifiedName~QueryCommandRunnerTests.RunStatus_CheckJson_ReportsLastFailedOrPartialIndexRun_Issue3567" -p:UseSharedCompilation=false
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~DocumentationStatusContractTests" -p:UseSharedCompilation=false
• dotnet build CodeIndex.sln -p:UseSharedCompilation=false
• dotnet run --project tools/CodeIndex.Changelog -- check
• git diff --check
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• Codex adversarial review: No blocking/actionable issues found.

Documentation and Changelog

• Updated README.md, USER_GUIDE.md, DEVELOPER_GUIDE.md, and AGENT_GUIDE.md.
• Added changelog fragments:
  • changelog.d/unreleased/3523.fixed.md
  • changelog.d/unreleased/3564.fixed.md
  • changelog.d/unreleased/3565.fixed.md
  • changelog.d/unreleased/3567.fixed.md

Follow-up Candidates

• None.

Fixes #3567
Fixes #3565
Fixes #3564
Fixes #3523