Preheat the oven to 350 degrees F. Line two baking sheets with parchment paper.
In food processor, pulse together 1 cup oats, flax seeds, arrowroot starch, Brewer’s yeast, cinnamon, baking soda, baking powder, and sea salt until finely ground. Dump into a large bowl, along with the remaining 2 cups of oats, the chocolate chips, and the pecans.
In the food processor (no need to clean out), combine the coconut oil and maple syrup and process on high for 2-3 minutes until light and fluffy. Add to the dry ingredients, and mix with a spatula until well combined.
Spoon heaping tablespoons onto the baking sheets. Wet hands slightly and lightly flatten the tops of the cookies (dough will feel a bit loose). Lightly sprinkle the tops with a bit of sea salt, if desired.
Bake for 12 minutes, until lightly browned. Let cool on cooling racks. When completely cool, store in an airtight container at room temperature, or put in a Ziplock freezer bag and freeze.
* You can use regular old-fashioned oats if you’re not gluten-free.