Merge branch 'doxy/commands'

* doxy/commands:
  Update documentation for doxygen tags
  Fix doxygen translation of \p command for python
  Fix doxygen handling of \em tag for python
  Minor formatting updates to doxygen docs
  Reformat tag lists in doxygen documentation
  Add doxygen_code_blocks_runme.java
  Special handling for python doctest code blocks
  Add new doxygen test doxygen_code_blocks
  Handle doxygen code command with language option
  Improve doxygen parser handling of \code content
  Flag optional arguments in doxygen pydoc output
  Add parameter direction to doxygen pydoc output
  Support doxygen \param[] commands