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Whisk together the flour, baking powder, baking soda, and salt in a large bowl. Add the chocolate to the flour mixture and toss to combine.
Combine the sugars with the oil, water, and vanilla extract in a separate large bowl and whisk briskly until smooth and incorporated, about 2 minutes. If there are sugar clumps, break them up with the back of a spoon or your hand before whisking.
Add the dry mixture to the wet mixture. Stir with a wooden spoon or a rubber spatula until just combined and with no flour visible. Do not over-mix.
Cover with plastic wrap. Refrigerate the dough for 6 to 12 hours. Do not skip this step.
Preheat the oven to 350°f / 180°c. Line two rimmed baking sheets with parchment paper. Remove the dough from the refrigerator. With a cookie scoop or spoon, portion the dough into 2 Tbsp mounds. Freeze for 10 minutes (optional).
Arrange the dough balls on a baking sheet (8 at a time works well for me). Sprinkle with flaky sea salt.
Bake for 10-12 minutes, until the edges are just golden, turning once to ensure even cooking. Do not over-bake.
Cool the cookies for 5 minutes, then move to a wire rack and allow to cool completely.
Store leftovers in an airtight container.