Replace qiime.util.DistanceMatrix with bipy.core.distance.SymmetricDistanceMatrix

:beers: **NOT READY FOR MERGE** :beers: 

This pull request removes ```qiime.util.DistanceMatrix``` and updates all related code to use ```bipy.core.distance.SymmetricDistanceMatrix```. Since this ended up being a huge number of changes, I'd like to get this reviewed/merged first, and I will then update the ```(labels, dm)``` tuple to use ```DistanceMatrix```/```SymmetricDistanceMatrix``` throughout the rest of QIIME.

Depends on https://github.com/biocore/bipy/pull/91 getting merged first.

Fixes #829.