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You can build freenect_stack with the version of freenect library installed by apt package manager.
Compiler could not find libfreenect/libfreenect.h, because after installation of libfreenect-dev package, the header file is located at /usr/include/libfreenect.h (note absence of libfreenect folder).
You can create symlinks for libfreenect header files to avoid messing around with the source code:
sudo mkdir /usr/include/libfreenect
sudo ln -s /usr/include/libfreenect*.h /usr/include/libfreenect/
I was able to build the package afterwards.
A quick test with RGB and depth images was fine.
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