Created by Marramamba on April 1, 2015
Step 1: Drain beans and place in a large heavy pot along with halved onion, Parmesan rind (if using), halved head of garlic, bay leaves, and 2 tsp. salt. Add water to cover by 2”. Bring to a boil, reduce heat, and simmer until beans are tender, 1–1½ hours.
Step 2: Meanwhile, cook bacon in a large skillet over medium heat, turning occasionally, until brown and most of fat has rendered, 8–10 minutes. Transfer to a plate with tongs or a slotted spoon.
Step 3: Add thinly sliced onion, shallot, thyme sprigs, and three-fourths of chopped garlic to pan drippings in skillet; season with salt and pepper. Cook, stirring occasionally, until onion is starting to caramelize and is very soft, 10–15 minutes. Add wine, bring to a simmer, and cook, stirring occasionally, until liquid is almost completely evaporated, about 4 minutes. Remove from heat and pluck out thyme sprigs.
Step 4: Preheat oven to 400°. Drain beans, reserving cooking liquid. Transfer beans to a large bowl and mix in bacon, onion mixture, thyme leaves, grated Parmesan, and 1½–2 cups cooking liquid (this will be most of it; mixture should be consistency of stew); season with salt and pepper. Transfer beans to a shallow 1½-qt. baking dish.
Step 5: Mix breadcrumbs, oil, and remaining chopped garlic in a medium bowl; season with salt and pepper. Scatter over beans; bake until liquid is thickened and bubbling and crumbs are golden brown, 45–55 minutes. Let cool slightly before serving.
Step 6: Do Ahead: Beans can be baked 5 days ahead. Let cool, cover and chill.