Improve documentation

[orome]

• Ask how to document list and optional returns and arguments (these don't render correctly).
  List[], list of ..., Optional[], ..., optional
• Ask how to get Yields to render correctly.
• Review how to do terms/definitions systematically.
• Review "overview" sections: Remove? Remove ~ for full names?
• Add and link mathematical discussion and equivalences; e.g., formula for ~.components.Component.mapping as: \mu_{i}(c)=\rho^{s_{i}(c)}\omega_{i}\rho^{-s_{i}(c)}
• Add example I'm machine mapping list of how in degenerate case first n are just the wiring (and explain stage as reverse too).
• Flesh out and link to sections.
• Review, fix, and document import organization.
• Fix figure background.
• Fix difference between how code for $ and code for >>> is formatted by RTD.
• Fix styles for deprecated functions?