Optic functions as arrays
Uses PyAT lattice for import
Adapt other files for the change

Update machines/__init__.py, machines/soleil.py, tracking/__init__.py, tracking/aperture.py, tracking/element.py, tracking/optics.py, tracking/parallel.py, tracking/particles.py, tracking/rf.py, tracking/synchrotron.py files

To be PEP8 complient:
Lowercase folders
Extended docstrings
Rename and divide some files