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The answer is that they were. Chazal learn this from Parashat Behar. If the commandment of Shemita, which had no application at all in the wilderness, was taught at Mt. Sinai explicitly, we learn all of the commandments were taught there (Rashi and Sifra).
Also, the location of a mitzvah in the text of the Torah has nothing at all to do with when it was ...
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