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Fix up warnings from doxygen

Aron Helser requested to merge aron.helser/smtk:api_doc_updates into master
  • 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.

@dcthomp @bob.obara

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