updated to correctly handle zero otus in the core

Fixes #642.
added doc on procrustes mapping file format
Merge pull request #953 from gregcaporaso/issue-642

updated to correctly handle zero otus in the core
text on procrustes sample id mapping file

Fixes #112.
generalized the documation of the sample id map file

didn't realize that this was being used in more places than just transform_coordinate_matrices.py
text clean-ups
text clean-ups
moved reference to more appropriate location
Merge pull request #955 from gregcaporaso/issue-112

Issue 112