commands: SECONDARY flag changes in cmd defs

commands: SECONDARY flag changes in cmd defs

Add/remove the SECONDARY_SYNTAX flag to cmd defs.
cmd defs with this flag will be listed under the
ADVANCED USAGE man page section, so that the main
USAGE section contains the most common commands
without distraction.

- When multiple cmd defs do the same thing, one variant
  can be displayed in the first list.
- Very advanced, unusual or uncommon commands should be
  in the second list.