DEP: deprecating PCoA, fixes #578
API: moved alignment.py to _alignment.py
API: moved pairwise.py to _pairwise.py
API: moved base.py to _base.py
API: replaced gini.py with _gini.py and lladser.py with _lladser.py
API: renamed base.py to _base.py
API: moved skbio.draw.distributions to skbio.draw._distributions
API: privatized anosim.py, base.py, permanova.py
API: privatized tree.py and trie.py
API: privatized skbio.alignment.ssw
API: privatized misc.py, _misc.handle_error_codes, _misc._get_create_dir_error_codes
API: privatized testing.py
API: privatized ordination methods
MAINT: fixes to imports
MAINT: flake8 fixes
MAINT: checklist.py fixes
Fix issues with ssw wrapper

Problem was relative imports, outdated .c file, and mismatched extension filenames vs extension name. Thanks @ebolyen!
Fix misnamed import in ssw_wrapper.pyx docstring
DOC: fix issues with skbio.draw docstring
DOC: skbio.util docstring clarifications