Fix Doxygen artifacts

[christophertubbs]

There are several issues with doxygen that just need to be cleaned up. For instance, there are mermaid graphs that show up great in github but not our github io page (https://noaa-owp.github.io/ngen/md_doc_2_g_i_t___u_s_a_g_e.html#autotoc_md173). We also have some pages that are split nicely, but not formatted well after the split (https://noaa-owp.github.io/ngen/md_doc_2references.html).

Doxygen settings and possibly markdown layouts just need to be tinkered with to make this a little prettier.