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Binary roots are the files which have historically been released by Apple as freeware (binary distributed and redistributable), but not as free software (source distributed, modifyable, and redistributable). They're intellectually encumbered or for some other reason, Apple can't release them. With the rafirafi's release of puredarwin 1.3 (on our News page), those have all been allegedly rewritten as free software as far as I know.