Phylesystem rename

Only merge this after https://github.com/OpenTreeOfLife/peyotl/pull/66 !
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.