Replacement for g_bond and g_dist.

Added a proper implementation for the 'distance' tool.
It should now do most of what g_bond or g_dist can do.
The help text related to the distance histogramming is somewhat
different from g_bond, but the behavior is more or less the same; now
the help text just describes how it is actually implemented.

The main things missing are proper legends in the output files, some
statistics output (g_bond), and g_dist -dist and g_dist -lt.
g_dist -dist can already be done with g_select, and g_dist -lt also
makes most sense to implement separately into g_select instead.

Part of #665.

Change-Id: I293cf8f0d30480e1873d5dcdef414f0089f177a6