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Why are Sh'kalim (Y'rushalmi) and Kinim and Midos (mishnayos) learned as part of the standard daf yomi cycle for Talmud Bavli?
And if the answer relies on some fact of publication, then (a) why were they published that way and (b) why did the founders of the daf-yomi system rely solely on that publication system instead of skipping those masechtos?
With regard to Sh'kalim, I believe the answer does indeed rely on publication practices. The practice of printing (and therefore studying) Sh'kalim with the rest of Talmud Bavli Seder Moed can be traced as far back as the times of the Geonim. [The idea is that Sh'kalim is short and therefore relatively inexpensive to print with the rest of Seder Moed to complete the entire seder, compared to something like completing Seder Zera'im with the Yerushalmi. (See here.)] Thus, the inclusion of Sh'kalim in the Daf Yomi cycle is simply a continuation of long-standing tradition of its study together with the rest of Talmud Bavli.
Tractates Midos and Kinim, though, are a separate issue. Why the completion of Seder Kodshim with mishnayos but not the other sedarim? The answer I've always heard given (as well as is speculated here) is that we attempt to finish Seder Kodshim based on the statement of the gemara in Menachos (110a): "When Talmidei Chachamim study the laws of the Temple service, it is considered as though the Beis HaMikdash was rebuilt in their days."
"What the Halacha is" is to found in "contemporary" anthologies such as Mishnah Brurara, etc.; HOWEVER "What is Halacha: is to be better understood from the Logic of Mesechet Kinnim (Avot 3-18 "R. Eliezer ben Hisma says...") wherein bird offering are the "easiest" practical example upon which to practice the logic of How much you can know without any doubt - even in the absence of simuhnim (identification detail) vrs Piske Nidah (onset of menstruation) where you discover how much you can still not know - even with a great abundance of simuhnim. This and That define the (limits of the) body of Halacha. SO - to answer this question: (CHAZAL appreciated that) "after you master the logic of Kinnim, then you will find every logical distinction - in every discussion - in every other part of SHAS to be much more transparent ("easier to understand")!
