Handle erroneous command line args better

Handle erroneous command line args better

Some gmx modules need to be able to accept non-option arguments, and
some should not. Introduced enough functionality to support such
behaviour, while giving useful error messages in cases where the
command line is merely missing hyphens (which can happen e.g. when
people copy-paste from inconveniently built PDF files for tutorials).
Increased test coverage of relevant cases.

Removed some useless command-line argument strings from test cases
that never needed them.

Also tested some behaviours of handling string options, and renamed
some test input strings to reflect the intent.

Fixes #2153

Change-Id: Icec02ea86a57a8b129a621121518036b9f032078