Baked Beans with Slab Bacon and Breadcrumbs
['2 cups dried navy or cannellini beans, soaked overnight', '2 medium onions, 1 halved, 1 thinly sliced', '1 Parmesan rind (optional), plus', '1/2 cup finely grated Parmesan', '1 head garlic, halved crosswise, plus 4 cloves, finely chopped, divided', '2 bay leaves', '2 teaspoons kosher salt, plus more', '8 ounce slab bacon, cut into 2x1/4" pieces', '1 large shallot, thinly sliced', '4 sprigs thyme plus 1 tablespoon leaves', 'Freshly ground black pepper', '1/4 cup dry white wine', '1 1/2 cups coarsely torn fresh breadcrumbs', '2 tablespoons olive oil']
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 teaspoons salt. Add water to cover by 2". Bring to a boil, reduce heat, and simmer until beans are tender, 1–1 1/2 hours.
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.
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.
Preheat oven to 400°. Drain beans, reserving cooking liquid. Transfer beans to a large bowl and mix in bacon, onion mixture, thyme leaves, and 1 1/2–2 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 1 1/2-quart baking dish.
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.
Do ahead: Beans can be baked 5 days ahead. Let cool; cover and chill.
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