DistanceMatrix -> DissimilarityMatrix, SymmetricDistanceMatrix -> DistanceMatrix

Still need to update unit test code.
fix doctest failing test
update distance module unit tests

Still need to update the rest of skbio to use the new class names.
update rest of codebase to use new names
Fix some minor issues with the docs
update "Gain in PD" reference
Remove specialized file format error classes

In favor of DissimilarityMatrixFormatError. Based on feedback from @gregcaporaso.
Merge branch 'master' into issue-242

Conflicts:
	skbio/maths/stats/distance/tests/test_anosim.py
	skbio/maths/stats/distance/tests/test_permanova.py
	skbio/maths/stats/ordination/test/test_ordination.py
SymmetricDistanceMatrix -> DistanceMatrix in merged code
Fix pep8 error
Merge pull request #245 from ElBrogrammer/issue-242

DistanceMatrix -> DissimilarityMatrix, SymmetricDistanceMatrix -> DistanceMatrix