Hi Robb, 
 
the buildpath issue is present on my system too. The generated files show:
  
  /* WARNING: This file is generated!
   * Do not edit this file, but edit /home/jaipaul/.../workspace/sources/doxygen/src/config.xml instead and run
   * python configgen.py -maph /home/jaipaul/.../workspace/sources/doxygen/src/config.xml to regenerate this file!
   */
  
  All three files — configvalues.h, configvalues.cpp, and configoptions.cpp — have the build path included.
  
The reason I missed it is that I used devtool upgrade and devtool build to build the recipe. devtool build only runs do_populate_sysroot and do_packagedata by default (hardcoded in scripts/lib/devtool/build.py),
  so do_package_qa never executed.
A normal bitbake doxygen would have triggered do_build which depends on do_package_qa, catching the error.
 
So, your patch is needed . 
 
Regards,
Jaipaul