Add 'gmx pairdist' tool as partial g_mindist replacement

Add a new tool that can compute pairwise distances from one reference
selections to one or more calculation selections.  The tool can do
minimum or maximum distance over the whole selection, as well as between
each residue/molecule pair in the selections.  This should provide
(nearly) all the distance outputs that g_mindist has, and with a bit of
effort also be able to replace g_mdmat.

The tool intentionally does not compute contact counts; those should be
added into a separate tool to keep things simpler.

Update some documentation references.

Change-Id: I553c3477ae808a133a3cec2b46feaccc3420022f