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It is not all in Shavout, there is some in Yevamot. I think the reason is because there is only about one or two perakim that are הלכה למעשה (like הרואה כתם) in Niddah, so the Rif wrote down the halachos thereof on masechtos that he was writing on anyway that have sugyas about Niddah, like the end of the second perek of Shavuot.