add script for collapsing replicate samples

**NOT READY FOR MERGE**

This needs a few things prior to merge:
 - [ ] port and test collapse functions
 - [ ] possibly generalize to replace ``summarize_otu_by_cat.py`` and take an ``axis`` parameter
 - [ ] needs biom > 2.1, so dependent on a release

This may ultimately make more sense to be part of BIOM, so may end up closing this PR without merge, but submitting now in case others have feedback.