Another merge with master.
Updated Doxygen error numbers yet again, as Python errors got added in the meanwhile, pushing the Doxygen ones further off. And re-merged PEP8/whitespace-related conflicts in autodoc_runme.py once again (if anybody is looking for a motivating example about why significant whitespace is bad, here is a great use case).
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doxygen_unknown_command.i:4: Warning 740: Doxygen parser warning: unknown command "unknown".
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doxygen_unknown_command.i:4: Warning 760: Doxygen parser warning: unknown command "unknown".
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