Fixed doxygen errors; no complaints remain.

There are, however, 4 warnings related to Doxyfile:
<pre>
2>CUSTOMBUILD : warning : Tag `SHOW_DIRECTORIES' at line 569 of file C:/Users/tkuchida/GitHub/opensim-core/build/Doxyfile has become obsolete.
2>  To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
2>CUSTOMBUILD : warning : Tag `HTML_ALIGN_MEMBERS' at line 1011 of file C:/Users/tkuchida/GitHub/opensim-core/build/Doxyfile has become obsolete.
2>  To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
2>CUSTOMBUILD : warning : Tag `USE_INLINE_TREES' at line 1202 of file C:/Users/tkuchida/GitHub/opensim-core/build/Doxyfile has become obsolete.
2>  To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
2>CUSTOMBUILD : warning : ignoring unsupported tag `EXTERNAL_SEARCH        =' at line 1275, file C:/Users/tkuchida/GitHub/opensim-core/build/Doxyfile
</pre>

Safe to do `doxygen -u` and clear out `EXTERNAL_SEARCH`? The former seems safe; not sure whether `EXTERNAL_SEARCH` is necessary.