Bring a saucepan half full of salted water to a boil over high heat. Add the pearl onions and cook for 2 minutes. Using a slotted spoon, scoop out the onions, rinse with cold water and drain. Reserve the water in the pot. Trim off the ends of each onion, then cut a shallow X into each trimmed end. Squeeze each onion gently to slip off the skin.
Bring the water back to a boil. Add the onions, reduce the heat to low and simmer, uncovered, until the onions are soft when pierced with a knife, 15 to 20 minutes.Using the slotted spoon, transfer the onions to a bowl. Continue to boil the cooking liquid until reduced to 1 cup, 15 to 20 minutes. Set aside.
Position a rack in the upper third of an oven and preheat to 375 deg. F.
In a saucepan over medium heat, melt 2 Tbs. of the butter. Add the minced onion and thyme and cook, stirring occasionally, until soft, about 7 minutes. Add the flour and cook, stirring constantly with a wooden spoon, until well mixed and bubbling, about 2 minutes. Add the reserved 1 cup cooking liquid, the milk and cream. Cook until the sauce boils and thickens slightly, 3 to 4 minutes. Add the nutmeg and season with salt and pepper. Add the pearl onions, adjust the heat to a gentle simmer and cook until the onions are hot, about 3 minutes.
Transfer the onion mixture to a 2-quart baking dish and sprinkle the bread crumbs evenly over the top. Cut the remaining 1 Tbs. butter into 6 equal pieces and dot the bread crumbs evenly with the butter. Bake until the crumbs are golden and small bubbles appear along the edges of the dish, 15 to 20 minutes. Serve immediately. Serves 6.
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