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It's like how all the core code of the Linux kernel is libre, but most of the versions distributed are proprietary, because to use them you are obliged to follow the license conditions of the binary blobs bundled with them.
Similarly, most GNU/Linux distros are proprietary, because while the majority of the code they're compiled from is libre, you can't run their without implicitly agreeing to the license terms of any proprietary binaries bundled with them.