Top-level global log flags should be covered by a tested CLI schema or completion contract

[Widthdom]

Problem

Top-level global log flags are parsed outside the query command schema/completion path, so they can drift from generated help/completion contracts.

Evidence

• src/CodeIndex/Cli/ProgramRunner.cs handles global log options such as --log-format, --log-retain-count, and --log-max-size-mb.
• Existing CLI flag schema tests focus on command-local schema/completion coverage, while these top-level globals are not visibly represented in the same tested contract.

Suggested direction

Add a top-level global flag schema/completion contract, include the log flags, and test that help/completions stay synchronized with the parser.

[Widthdom]

Work started on branch fix-issue3226.