Separate lib from cmd

I separated the main align code to `align.py` from `bleualign.py`, and moving all global variables into `Align` as class members.  Packaging will be easy after refactoring.

I think data in eval directory is designed for running commands not for libarary, so I moved `options['eval']` in `util.py` into `load_arguments`.

Commands like `bleualign.py` and `batch_align.py` also keep unchanged.