Preheat your oven to 350°F (177°C). Place a rack in the top third of the oven at least 6 inches (15 cm) from the heat source and cover your baking sheets with parchment paper.
Put the butter in a medium saucepan and melt over medium heat. Once melted, crank up the heat to medium high. Continue stirring and look for small golden bits that will start to settle on the bottom of the pan. It will smell deliciously nutty and caramel-y. This should take around 3 to 5 minutes. Once this happens, take it off the heat and pour into a large, heat-safe bowl to cool a bit.
When cooled slightly, whisk in the brown sugar, granulated sugar and oil. Once smooth, add in the eggs one at a time, completely mixing in the first before adding the second. Whisk in the vanilla until blended. Be sure to scrape down the sides and bottom of the bowl to make sure everything is incorporated.
In another medium bowl, whisk together the all-purpose flour, bread flour, baking powder, baking soda and sea salt. Add this to the brown butter mixture and mix until just combined and you still see streaks of flour. Add in the chocolate chunks, quinoa, cherries and pecans and continue to blend until just combined. This dough is loaded with goodies and some may have a hard time adhering to the dough. Just force them back in there.
Gently roll 2 tablespoons (28 g) of dough into a ball. Place the dough balls on the covered baking sheet about 2 inches (5 cm) apart and press down slightly to form discs. Sprinkle each with a pinch of sea salt flakes, if using.
Bake one sheet at a time for 11 minutes in the top third of the oven. Let the cookies cool for 10 minutes on the baking sheet, and then transfer to a rack to finish cooling.