CMake: install headers into the proper sudirs

The CMakeLists.txt was installing everything in the
same directory, instead of creatin the proper subdirectories.

Modified the CMake to extract the path of the file and use the
path without the "src/" in the INSTALL()

Thanks to harmony-ek (github) for pointing it out.

Signed-off-by: Luca Fulchir <luker@fenrirproject.org>