I'm working on a C++ project that uses autoconf & automake , and I'm struggling to correctly set up the include paths in *CPPFLAGS . I've read about 3 hours worth of documents, and I can't figure it out yet. I'm not looking for a hack, but for the correct way to do this. Here is my conundrum. As I see it, there are 3 completely different sources for include paths: External libraries that must be installed along with my package, which are configured by configure --with-XXX=<PATH> . Within my package, some source files use #include <file.h> even when file.h is part of the package, so to compile