create alignment submodule

~~**NOT READY FOR MERGE**  Working on some doc issues, but I want travis to run the tests in the meantime.~~

Doc issues sorted out, I think this should be ready to go, but we need to remember to test install/testing with setup.py before the release since I did have to make changes to setup.py. 

Fixes #419.

See note above about importing directly from `ssw_wrapper`.