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.

Like above, I think this should import the objects from `ssw_wrapper.pyx` that way the folder can be treated as a file which contains it's own dependencies.