MAINT: created submodule for better organization

see #419.
MAINT: moved ssw into new alignment sub-module
removed old init
MAINT: updated references
MAINT: removed to reflect new location of docs
MAINT: removed to reflect new location of docs
updated paths/modules for ssw install
MAINT: fixed typo, thanks @ebolyen
Merge pull request #430 from gregcaporaso/issue-419

create alignment submodule