update doxygen file
don't check template headers for header guard

it is almost impossible to get right and there is no reason for it to be right
Split up doxygen runs into one per module

This makes testing a particular documentation change much, much faster, so hopefully people will actually look at it.

close #357, close #366
remove useless pythonexample doxygen command
remove impsvn command
remove some more unused doxygen commands
examples should now be included directly
clean up some more includes
clean up some doc problems
suppress em doc warnings

close #364
fix file name
example kernel readme
fix typo
we actually aren't doing that
remove duplicate doxygen paths
suppress doxygen warning
doxygen produces troubling warning messages when run in parallel from the same dir

warnings about doxygenXXXX.tmp not being found, implying there is some interaction between runs. Run each doxygen copy from a separate dir. This makes doc generation even more windows unfriendly
don't suppress files called test_* as those kill test_macros.h
make documentation as part of ALL to encourage people to worry about warnings in it
don't list external pages

we might instead want to go to YES for all the external options,
but lets try NO for now.