add markdown and styling notes

docs/README.md

@@ -79,3 +79,33 @@ run in the command line as
 cd path/to/repo/
 doxygen Doxyfile
 ```
+
+### Markdown
+
+[Doxygen supports Markdown!](http://www.doxygen.nl/manual/markdown.html) So you can use markdown in comment blocks if necessary.
+
+In the doxygen file you can also point the frontpage to a `.md` file.
+
+```make
+USE_MDFILE_AS_MAINPAGE =
+```
+
+This will populate the mainpage with html from the specified markdown file.
+
+### Custom Output
+
+
+You can specify a html header, footer and custom css files. The easiest approach would be to generate these first
+
+```sh
+doxygen -w html header.html footer.html customdoxygen.css
+```
+then edit them as necessary.
+
+Change these options in the Doxyfile
+
+```make
+HTML_HEADER = header.html
+HTML_FOOTER = footer.html
+HTML_EXTRA_STYLESHEET = my_customdoxygen.css
+```