Bring in some simple fixes from ctsm1.0.dev006 and avoid glacier adjustment at startup from ctsm1.0.dev007

Bring in a list of simple fixes that came to CTSM master. Also change so glacier initialization is ALWAYS done
at startup (time step zero) even if it isn't cold or interpolated initial conditions. Also synchronize some of the
files in the doc directory with the files in ctsm/master.

This is a duplicate of the release-clm5.0.06 tag, but properly on the release-clm5.0 branch. The previous tag was stand-alone.