Move command listing to 'gmx help commands'

Instead of printing the list of commands on 'gmx' or 'gmx help', print
it only when explicitly requested with 'gmx help commands'.  This makes
it easier to see the help about the common command line options that
'gmx' accepts.  The list of available help topics lists the 'commands'
topic, so it should be easy to find.

Related to #685.

Change-Id: I00e9ceae15ebd47d2ac129aae8e6e407f86c388a