Rename hmm and msm modules

hiddenmarkovmodel -> hmm
markovstatemodel -> msm
Add aliases for backwards compatiblity
Update setup.py for new extension locations
Update tests
Update relative imports
Missed a relative import
Merge pull request #285 from mpharrigan/moves_and_aliases

Moves and aliases
Fix doc building
Shuffle gitignore
Change all notebook paths to examples/nb.ipynb
Update example notebooks