Draft: Remove HideHelpCommand: true from all commands

Addresses: #5485

It seems there has been a change since that issue was raised and we are showing the COMMANDS list again. This is causing some duplication in the help text since we are manually mentioning the subcommands as well.

This MR removes the manual mentions and adds back the help sub command since it seems to be working now.

Before

$ praefect configuration --help
NAME:
   praefect configuration - manage configuration

USAGE:
   praefect configuration command [command options]

DESCRIPTION:
   Manage Praefect configuration.

   Provides the following subcommand:

   - validate

COMMANDS:
   validate  validates configuration

OPTIONS:
   --help, -h  show help

After

$ ./_build/bin/praefect configuration  help
NAME:
   praefect configuration - manage configuration

USAGE:
   praefect configuration command [command options]

DESCRIPTION:
   Manage Praefect configuration.

COMMANDS:
   validate  validates configuration
   help, h   Shows a list of commands or help for one command

OPTIONS:
   --help, -h  show help