In a mixing bowl, whisk together the flour, salt, baking powder, baking soda, cinnamon, ginger, and nutmeg.
Melt the butter in a large, microwave safe bowl. Add the sugars and whisk together until smooth. Whisk in the pumpkin puree and vanilla extract.
Add the flour mixture and stir with a spatula until the batter comes together and the powder is incorporated. The dough will be very thick. Stir in the chocolate chips and pecans. Cover the batter with saran wrap and refrigerate for at least one hour or overnight.
Remove dough from the refrigerator. Note: if refrigerating more than 1 hour, you will need to let the dough sit out at room temperature for at least 15 minutes before scooping. A longer refrigeration might need to sit out for up to 30 minutes to be scoopable).
Preheat the oven to 350 degrees and line two baking sheets with silicone mats or parchment paper. Scoop Tablespoon size balls of dough onto the prepared sheets. Flatten each scoop into a 1/4-1/2 inch thick disc with your palm or the bottom of a glass. Bake for 10-12 minutes, rotating the pans halfway through. The cookies should look set on the outside but still a bit soft in the middle. Remove from the oven and allow to set up on the tray for another 5 minutes before removing to a wire rack to cool completely.