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I've seen several Makefiles and build scripts that invoke `pkg-config --cflags gtk+-3.0` for example. I think it would be fairly easy to create an output parser that detects the pkg-config pattern, executes `pkg-config --cflags gtk+-3.0` then parses the output to detect includes (reusing output parser).
I uploaded a small prototype here in case anyone needs this before I get to finish it: https://github.com/MarkZ3/Eclipse-CDT-WIP/tree/PkgConfigOutputParser