[v3] testsuite vs. cxxflags, others

[Benjamin Kosnik]

This is a merge from my active tree.

- make CXXFLAGS="-D_GLIBCXX_DEBUG" check
works now, for various CXXFLAGS

- some formatting

- for ext headers, be pedantic about including std headers

- doxygen updates for new directory structure

- test file fixups for debug mode

tested x86/linux

-benjamin
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