BUG: Fix bug in make_distance_comparison_plots

This bug would create empty groupings in a plot when sample ids appeared
in the mapping file but didn't appear in the distance matrix.

The code also checks for cases where samples are not shared between
mapping file and distance matrices.

Fixes #1534
Merge branch 'master' of git://github.com/biocore/qiime into issue-1627

Conflicts:
	ChangeLog.md
:lipstick: beautify thy codeness
MAINT: Undo previous change about shared samples
DOC: Fix documentation error
Merge pull request #1788 from ElDeveloper/issue-1627

BUG: Fix bug in make_distance_comparison_plots