Adds a topological_generations function and refactor topological_sort
to yield from topological_generations.

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
Co-authored-by: Dan Schult <dschult@colgate.edu>

* Fixes #3955 (boundary_expansion docs)

* add to docs for steiner_tree

* Add missing functions to docs. Thanks to #4111

* Doc fixups

* Put filters onto the doc pages.

* Add @jamestrimble doc compare script to repo and expand

* Fix latex syntax in docs for trophic

* more latex corrections

* deprecate edge_betweeness and betweeness_centrality_source.

warnings and add to list of deprecations

* Use docs to identify hopcrfot_karo_matching and maximum_matching

* remove  underscore from _naive_greedy_modularity_communities

* cite James Trimble for code that finds missing functions

* Update parallel_betweenness example to avoid deprecated function

betweenness_centrality_source should be replaced by
betweenness_centrality_subset in plot_parallel_betweenness.

find _naive_greedy and change name

* tweak

* Update docs with all functions not added to rst files

Also add script to find these functions

* put back removed periods after references

This is #2060 with conflicts resolved.  Fixes #2060

This commit adds two new functions and an example application using
those functions.

- The `prefix_tree` function (in the new module
  `networkx/generators/trees.py`) generates a prefix tree (aka a trie)
  from a given list of strings (or integers, etc.).
- The `dag_to_branching` function in `networkx/algorithms/dag.py`
  creates the branching that results from interpreting the list of all
  paths from root nodes to leaf nodes in the DAG as the root-to-leaf
  paths in a prefix tree.
- The example application of the `dag_to_branching` function, in the
  `examples/applications/circuits.py` module, demonstrates how to
  convert a Boolean circuit into an equivalent Boolean formula.

* Finish directory reorg and make minor text edits

* Remove cruft from conf.py

* Fix broken links and comply with pep8