Nexus: refactor to become a true Python package

[jtkrogel]

Nexus currently uses PYTHONPATH=/path/to/nexus/lib/ to "install", where lib contains all the python files.
This style pollutes the general Python environment (i.e. from structure import read_structure then always pulls from Nexus).

Instead, Nexus should be upgraded to be a proper Python package where PYTHONPATH should point to a directory containing __init__.py with Nexus restructured to support standard nested imports, i.e. from nexus.structure import read_structure and/or import nexus as nx followed by local usage of nx.structure. This way, only the top-level module name nexus is exposed to the general Python environment.