Whisk the melted ghee, maple syrup, brown sugar and plain Greek yogurt together in a medium bowl until no brown sugar lumps remain. Whisk in the vanilla and blotted pumpkin until smooth. Set aside.
Whisk the whole wheat flour, oats, salt, baking powder, baking soda, cinnamon, and pumpkin pie spice together in a large bowl.
Pour the wet ingredients into the dry ingredients and mix together with a large spoon or rubber spatula. The dough will be very soft. Fold in 1/3 cup dark chocolate chips and 1/4 cup pepitas (if desired). The chips may not stick to the dough because of the melted butter, but do your best to combine them. Cover the dough and chill for 30 minutes or up to 3 days. Chilling is mandatory.
Preheat oven to 350 F.
Remove dough from the refrigerator. Line one large or two medium baking sheets with parchment paper or silicone baking mats.
Use a cookie scoop to make the dough into balls, about 1.5 Tbsp per cookie. Using the back of a spoon, slightly flatten the tops of the dough balls. (Without doing so, the cookies may not spread.)
Bake for 10-14 minutes or until the edges appear set. The cookies will look very soft in the center. Remove from the oven. If you find that your cookies didn’t spread much at all, flatten them out with the back of a spoon when you take them out of the oven.
Cool cookies on the baking sheets for at least 10 minutes before transferring to a wire rack to cool completely. Sally's Baking Addiction Says: "The longer the cookies cool, the even better they taste! The flavor gets stronger and the texture becomes chewier. I usually let them sit, uncovered, for several hours before serving. Chewiness and pumpkin flavor are even stronger on day 2."
Store cookies in an airtight container in the refrigerator for 3-5 days, or transfer to the freezer in a freezer-safe Ziploc bag. They thaw well if you pop them in the microwave!