Fix up warnings from doxygen
- Incorrect directory paths
- Missing file and namespace docs
- Unquoted code fragments
- Use of <>, which is interpreted as html
Change to WARN_IF_UNDOCUMENTED = NO in doxygen settings - there are far too many undocumented warnings for this setting to be useful. If a developer adds doxygen docs, they need to see if there are warnings about the new docs.