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Whisk together the flours, baking soda, cinnamon and sea salt in a bowl. Beat together the margarine, sugar and molasses on medium speed in a mixer until light and fluffy (scrape down sides). Add the flour mixture and mix until well incorporated.
Roll out 1/8-inch thick on a baking sheet and use a cutting wheel to cut into rectangles and prick with fork. Transfer each cracker to an ungreased baking sheet using a spatula, spacing them about 1 inch apart. Bake until golden brown, 15 to 18 minutes, rotating halfway through. Cool completely (crackers will be crisp).