Phylesystem rename

Only merge this after PR https://github.com/OpenTreeOfLife/peyotl/pull/69 !
After that point this will be just one commit.

This just breaks one file into 4 to make it easier to deal with. The important Phylesystem class is now defined in a new location in the code, but the peyotl/phylesystem/init.py imports it. So client code does not have to change to find it. The other classes and functions that had been in init.py should have been private all along, so client code should not have been referring to them.