fix requirements, enable nitpicky mode

Enable Sphinx's nitpicky mode. Sphinx will now warn about all references to missing objects. Fix some of these broken references, and ignore others. Sphinx now produces 7 warnings instead of the ~40 prior to the PR.

To generate a graph of entity dependencies, one should have the normal graphviz program installed, not the graphviz python module. Update the readme file to state this, and remove "graphviz" from file `requirements-optional.txt`.