1. Roll out the puff dough in a circle 1/8-inch-thick to fit a 12 inch tart pan. Press the dough into the pan well and chill in the refrigerator until firm, about 1 hour. Preheat the oven to 400 degrees F.
2. Remove the lined tart pan from the oven. Prick the dough well with a fork and line it with a single sheet of aluminum foil. Use pie weights or beans to weight the foil. Place the tart pan and bake for 20 minutes until the dough is lightly golden on the edges. Remove the tart shell from the oven. Remove the weights and the foil and place back in the oven for 10 more minutes or until the tart shell is golden. Cool on a rack. The tart shell can be baked up to two days in advance. Thoroughly cool, wrap tightly in plastic and store at room temperature.
3. Peel, remove the root core and cut the onions in half vertically from root end to point. Slice the onion halves into thin wedges.
4. Heat a 5 quart pot over medium heat. Add the olive oil and then the sliced onion. Cook the onions until wilted and beginning to sweat their liquid. Stir frequently to prevent hot spots and browning. Add the honey and thyme and season with salt and pepper.
5. After the onions have lost their volume and are soft. Reduce the heat to low and cook the onions, stirring occasionally, until all the liquid in the pan has evaporated, about 50 minutes. The onions will lose their pallor and turn a pale gold. Their texture will be meltingly tender. Spread out on a pan to cool. The onions may be cooked up to a week in advance. Store in a sealed container under refrigeration.
6. Preheat the oven to 350 degrees F. spread the cooked onion evenly in the bottom of the prepared tart shell. Whisk the crème fraiche with the egg and season with 1/2 teaspoon salt and a few grinds of pepper and pour over the top of the onions. Crumble the bacon over the top and bake in the preheated oven for 25 to 30 minutes until the crème fraiche is golden and set. Remove from the oven and cool to warm. Sprinkle with chopped chives before serving.
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