Remove remaining uses of programs.txt

Other uses have been replaced with direct generation from the wrapper
binary.  Since the manual no longer has the program man pages, there is
no particular need to list the programs either, in particular since this
is potentially more maintenance.  A reference to the online help and/or
'gmx help' should be sufficient.

Related to #685.

Change-Id: Ie865e955416cdc28f654cf2f988994bac7550ac6