Use longer imports in favor of convenience imports

Instead of using ``from skbio import foo`` we now use the longer form of the import in order to avoid the chance of circular imports happening. For example, ``from skbio import DistanceMatrix`` becomes ``from skbio.stats.distance import DistanceMatrix``.

The ``skbio.io`` additions prompted these changes but this was a problem waiting to happen regardless of the I/O system. Unit tests and doctests should still use the shorter/convenience imports as these are testing our user-facing API and we don't have the risk of circular imports there. All skbio library code should use the longer imports though.

@ebolyen can you please review?