[codex] Fix issues 3681, 3683, 3689, 3690, 3715

[Widthdom]

Summary

• Consolidate MCP bounded JSON response/audit stream handling.
• Share long-path-safe filesystem write probes across indexing and CLI paths.
• Report unknown-extension sample limit metadata in export/import JSON.
• Route non-trivial CLI environment reads through the scoped environment abstraction.
• Route command-facing stderr diagnostics through the shared error sink.

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Debug -p:UseSharedCompilation=false --filter "FullyQualifiedName~McpServerTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Debug -p:UseSharedCompilation=false --filter "FullyQualifiedName~FileIndexerTests|FullyQualifiedName~GitHelperTests|FullyQualifiedName~GlobalToolLogTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Debug -p:UseSharedCompilation=false --filter "FullyQualifiedName~ExportImportCommandRunnerTests|FullyQualifiedName~ProgramCliTests.ExportArchive_ManifestIncludesReadinessAndSummaryMetadata_Issue3549"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Debug -p:UseSharedCompilation=false --filter "FullyQualifiedName~ConsoleUiTests|FullyQualifiedName~GlobalToolLogTests|FullyQualifiedName~ProgramRunnerTests|FullyQualifiedName~FileIndexerTests|FullyQualifiedName~DbReaderTests|FullyQualifiedName~CdidxConfigFileTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Debug -p:UseSharedCompilation=false --filter "FullyQualifiedName~HookCommandRunnerTests|FullyQualifiedName~DbDebugTests|FullyQualifiedName~CommandErrorCodesTests|FullyQualifiedName~CodeIndexExceptionTests|FullyQualifiedName~QueryCommandRunnerSearchTests|FullyQualifiedName~ProgramRunnerTests|FullyQualifiedName~McpServerTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Debug --no-build --framework net8.0 --filter "Issue3681|Issue3683|Issue3689|Issue3690|Issue3715"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Debug --no-build --framework net9.0 --filter "Issue3681|Issue3683|Issue3689|Issue3690|Issue3715"
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• Codex adversarial review: no blocking or actionable issues found.

Fixes #3681
Fixes #3683
Fixes #3689
Fixes #3690
Fixes #3715