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To prepare the caramelized onions: In a large nonstick skillet, melt the butter over medium heat. Add the onions and cook, stirring occasionally, until they soften and begin to turn golden brown, about 10 minutes.
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Reduce the heat to medium-low and continue cooking, stirring every few minutes, until the onions are deeply caramelized, 25 to 30 more minutes.
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Stir in the red wine vinegar, thyme, pepper, and salt. Cook for 1 to 2 minutes more, just until the vinegar is absorbed and the mixture is fragrant.
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Remove from the heat and allow the onions to cool to room temperature; spreading them into a thin layer on a plate or baking sheet can shorten this process to about 10 minutes. (Caramelized onions can be made up to 5 days in advance and stored, covered in the refrigerator, until ready to use.)
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While the onions cool, preheat the oven to 375°F with a rack in the center. Lightly grease a baking sheet, or line it with parchment.
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To make the dough: In a large bowl, whisk together the flour, baking powder, sugar, thyme, salt, and pepper. Using your fingertips, a fork, or a pastry blender, work in the butter to make an unevenly crumbly mixture; it's OK for some larger, pea-sized chunks of butter to remain unincorporated. Mix in the Gruyère and cooled caramelized onions, tossing to coat in the flour mixture.
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In a small bowl or liquid measuring cup, use a fork to whisk together the cream, eggs, and mustard. Add to the dry ingredients and use a flexible spatula or bowl scraper to quickly and gently mix until a shaggy dough forms; some dry bits are OK.
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Transfer the dough to a lightly floured work surface. Fold the dough over onto itself two to four times to incorporate any remaining dry bits and form a cohesive dough; if the dough sticks to the surface or your hands, sprinkle with additional flour as needed.
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Pat the dough into an 8" disk (about 3/4" thick). Use a chef's knife or a bench knife to slice the dough into eight evenly sized wedges (about 100g each).
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Transfer the scones to the prepared baking sheet, leaving at least 1" of space between them. Brush the tops with the egg wash and sprinkle with additional pepper.
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Bake for 20 to 25 minutes, until the scones are golden brown on top and around the edges. Remove from the oven and serve warm or at room temperature.
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Storage information: Store leftover savory scones, well wrapped, at room temperature for several days. Freeze for longer storage. Scones are best when rewarmed before serving.