Overview docs for using Gromacs as a library

Add some documentation for the commandline module, and make the set of
installed headers provide a useful set of features.
Add an overview documentation for how to initialize Gromacs as a library
under different contexts.  Also, include some general notes about the
Gromacs API.  Can be extended in the future.

Change-Id: I13921fe1f1434fee8c495a169e6f5db645711f79