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OK, there are a lot of autoconf scripts that are poorly written, and therefore don't get the benefits. I've never heard of waf. I've never had to fight with scons, but I've never used it for my project.

But, for the love of all that is holy, do not CMake. It works fantastically... until you have to fix something. I tell you this as a distro packager. I've had to fight with build systems. Patching autoconf files, automake files, ant files, are all fairly comfortable for me. I dread the days when I have to figure out an issue with CMake.

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