Fix requirements-optional.txt

To generate a graph of entity dependencies, the graphviz python module is not
required. Instead, the user should have the normal graphviz program installed.
Update both the documentation and requirements file to reflect this fact.
Enable Sphinx's nitpicky mode

Make Sphinx warn about all references where the target cannot be found. Fix some
of those references, and make Sphinx ignore others (e.g. to the "str" target).
Merge pull request #985 from Ichimonji10/docs

fix requirements, enable nitpicky mode