Function applyRootVisibility

Apply root option visibility to the provided program instance. Flags set to false in the visibility map are hidden via hideHelp(true).

Help-time only:

• This affects rendering of top-level help; it does not alter parsing or runtime semantics.

Families vs singles:

• Families (e.g., "shell") hide both ON and OFF flags.
• Singles (e.g., "capture") hide the named long flag only.