Remove skbio.core from import paths

~~**Not ready for merge!** I'd like to see the tests run while I fix a few remaining stylistic issues.~~ Ready to go once tests pass.

``alignment``, ``distance``, ``genetic_code``, ``sequence``, ``tree``, and ``workflow`` are now top-level subpackages/modules.

Fixes #567.
Note for posterity:
This change prevented 'sideways' leaks where a test would be told to prefer an import that was shorter, but only by virtue of being imported from a different unrelated module and NOT from an API sanctioned __init__