API: removed math, skbio.math.$ -> skbio.$

fixes #541

Summary of changes:

`skbio.math` was removed.
`skbio.diversity` and `skbio.stats` replace this.

`gradient.py` was moved to `skbio.stats`
`stats/misc.py` became private
`stats/subsample.py` was moved to a directory and became private.
Not necessary to take care of in this PR, but we'll need to rename this module (and several other "private" modules) to have a leading underscore (see #562 for details).