Make PICRUSt compatible with BIOM v2

Update code to BIOM 2.0.1

Output from predict_metagenomes.py and normalize_by_copy_number.py
give the same output as before changes.

However, tests need to be updated and some metadata may not be transferred over
correctly. (several tests are currently failing)

Later commits should fix tests, but should wait for BIOM 2.1 to be released.