explain doxygen design pattern

README.md

@@ -12,3 +12,11 @@ Do not push any edits to the `gh-pages` branch as these will be overwritten.
 Instead, commit your changes to the `master` branch, and the `gh-pages` branch
 will be updated automatially a few minutes later. The documentation source is
 in `docs/source/` and the html source for the cover page is in `docs/webroot/`.
+
+### Doxygen
+
+Whenever the online documentation is updated, a fresh doxygen will be generated
+also. Note that the configuration in `docs/doxygen/doxygen.conf` specifically
+prevent source code from being displayed. This is by design. If you want to
+create your own private doxygen containing the source code also, please
+configure and run the `doc/Doxyfile.in` in your clone of the MFiX-Exa repo.