Fix time provider and suggestion timestamps

[Widthdom]

Summary

• Added injectable TimeProvider seams for time-sensitive CLI/MCP paths, including status age calculations, query trace/log naming, MCP ping timestamps, and suggestion-store submission timing.
• Moved suggestion CreatedAt stamping into the locked persistence path so the stored timestamp reflects when the record enters the local store.
• Replaced brittle hardcoded test datetime fixtures with a shared manual test clock where the affected tests depend on relative freshness.
• Stabilized diagnostic stderr writes for closed/disposed CI writers and preserved the public SuggestionStore constructor.

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~SuggestionStoreTests|FullyQualifiedName~ConsoleUiTests.TryWriteErrorLine|FullyQualifiedName~McpServerTests.RunAsync_InitializeEmitsInitializedNotificationAfterResponseOnlyOnce|FullyQualifiedName~McpServerTests.RunAsync_StdioCancellationNotification_CancelsActiveRequest|FullyQualifiedName~McpServerTests.RunAsync_StdioEofDrainsInFlightRequestBeforeReturning|FullyQualifiedName~McpServerTests.RunAsync_ShutdownNotification_DrainsAndExits|FullyQualifiedName~ConcurrencyTests|FullyQualifiedName~LegacySchemaMigrationTests|FullyQualifiedName~McpServerTests.ToolsCall_Ping_ReturnsVersionAndTimestamp" (net8.0/net9.0: 94 passed each)
• dotnet run --project tools/CodeIndex.Changelog -- check
• git diff --check origin/main..HEAD
• Adversarial review: No blocking/actionable issues found.

Notes

• Full McpServerTests was not used as final validation because unrelated git commit tests attempted to use the local signing key and failed on passphrase prompt.
• Full index refresh still hits the existing extraction stall tracked by Full index can stall on current repository after branch refresh #2717.

Changelog

• changelog.d/unreleased/1617.fixed.md
• changelog.d/unreleased/1618.fixed.md
• changelog.d/unreleased/2034.fixed.md

Fixes

Fixes #1617
Fixes #1618
Fixes #2034