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It looks like the CMake Eclipse generator does not include these paths, because they are implicitly included by the compiler. It looks like you can either add them to you include path manually within CMake or you can globally configure eclipse to include them.

http://stackoverflow.com/questions/1564668/cmake-and-eclipse-default-include-paths

From that post, it seems like the suggestion is to add it to eclipse globally, as they pointed out it is redundant (and not portable) to put these paths in CMake manually and is not necessary as the builds succeed. Rather I think the better solution is to globally configure eclipse to add those by default for autocompletion and syntax checking purposes.