Preheat the oven to 350 degrees F. Grease six 8-ounce ramekins with butter and set aside on a rimmed baking sheet.
Cut six 1/2-inch thick slices from the baguette and place them on the baking sheet. Cut the remaining baguette into 1/2-inch cubes (you should have about 4 1/2 cups) and spread them out on the same baking sheet. Bake, tossing the cubes and flipping the slices halfway through, until lightly browned, about 15 minutes.
Meanwhile, melt the butter in a large skillet over medium-high heat. Add the onions, thyme, 1 teaspoon salt and a generous amount of black pepper and cook, stirring occasionally, until the onions begin to soften, about 6 minutes. Reduce the heat to medium-low and cook, stirring occasionally, until the onions are very soft and caramelized, 35 to 40 minutes. Add the wine, turn the heat to medium-high, bring to a boil and cook until the wine has evaporated, about 5 minutes. Add 2 cups water and the bouillon cube and stir until the cube dissolves. Bring the mixture to a boil and let cook until thickened slightly, about 5 minutes.
Whisk together the heavy cream, chives, eggs and 1/2 teaspoon salt in a medium bowl. Add 1/2 cup bread cubes to each ramekin, sprinkle each with 1/4 cup Gruyere and top each with 1/4 cup bread cubes. Pour the egg mixture over the top. Divide the onion mixture among the ramekins. Top each ramekin with a slice of bread and 3/4 cup Gruyere.
Set aside at room temperature for 15 minutes to allow the bread to absorb the egg mixture. Bake on the baking sheet until the custard is set and the bread pudding is puffed and golden, about 20 minutes. Let stand 5 minutes before serving.
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