Start building custom extension for documentation

Clean up license, manifest, readme (which I thought
I deleted during the doc cleanup)
Small refactor in support of doc building

- Change top_name to be the name of the class in topology.py
- Get rid of keywords list. Instead use keyword_aliases.keys()
- Make the target field the actual name of the property
- Change top_name et al to be class methods
Auto-generate atom selection docs
Move element selection to new class

- Add test
- Add docstrings to element properties
Add some documentation
Templates for properties

- Add some not-implemented properties
- Make existing docstrings better