Fix top-level log flag schema coverage

[Widthdom]

Summary

• Added top-level scope to CliFlagSchema and derive ProgramRunner global parser flag sets from it.
• Surface --log-format, --log-retain-count, and --log-max-size-mb in help and bash/zsh/fish/PowerShell completions.
• Added schema/completion tests that guard parser drift for the top-level log flags.

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --configuration Release --framework net9.0 --filter "FullyQualifiedName=CodeIndex.Tests.McpAuditLogTests.ToolsCall_TruncatesAuditRequestId_Issue3237"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --configuration Release --framework net9.0 --filter "FullyQualifiedName~McpAuditLogTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~CliFlagSchemaTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~ConsoleUiTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~ProgramRunnerTests"
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet format CodeIndex.sln --verify-no-changes
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll . --json
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• dotnet test passed before merging latest origin/main; after conflict resolution, a full rerun was stopped after 19m+ with no failure output, while the targeted tests above passed.
• Adversarial review: No blocking/actionable issues found.

Docs and Changelog

• Updated CLI help output for top-level log flags.
• Added changelog.d/unreleased/3226.fixed.md.

Related

• Refs MCP audit request-id truncation test conflicts with JSON-RPC id length cap #3306

Fixes #3226