Update doxyfile for version of doxygen used by CI, turn on some settings...

[edwardhartnett]

The doxyfile is generated by cmake from docs/doxyfile.in. Variables in doxyfile.in like @Version@ are replaced with the appropriate values by cmake.

We need to:

• learn the version of doxygen used by GitHub CI.
• get on a machine with that exact version of doxygen (or install that version).
• cd docs and run doxygen -u Doxyfile.in to update the Doxyfile.in file. This will add some settings and comments.
• push changes and submit PR with new Doxyfile.in.

The end result will be an updated doxyfile.in, which includes some new fields.

See ufs-community/UFS_UTILS#418 for an example.

Then, we want to set the following:

• set REFERENCED_BY_RELATION = YES if you want the documentation for each subprogram to include a list of which other subprograms call it
• set REFERENCES_RELATION = YES if you want the documentation for each subprogram to include a list of which other subprograms it calls

[kgerheiser]

Why does the Doxygen version matter, or rather why does it have to be the same version?