Place beans in a large bowl and cover with 4 cups water; let soak overnight.
Drain beans and transfer to a medium saucepan; cover with water by 2 inches. Bring water to a boil, reduce heat and skim foam from surface. Continue simmering beans until tender, 30 to 45 minutes, adding more water as necessary. Season beans with salt and set aside to cool in their liquid.
Preheat oven to 350 degrees. In a medium, heavy-bottomed skillet heat 1/4 cup of olive oil over medium heat. Add onion, carrot, and celery; cook until tender, about 10 minutes. Add garlic and sage, and season with salt; let cook 5 minutes. Stir in tomatoes; cook 5 minutes more and remove from heat.
Drain beans, reserving liquid. Transfer beans to skillet with vegetables; stir to combine. Pour bean mixture into a medium gratin or baking dish; season with salt. Add enough bean cooking liquid to almost cover. Drizzle with olive oil and top with toasted breadcrumbs.
Transfer gratin dish to oven and bake for 40 minutes, checking occasionally to make sure the gratin has not dried out. If necessary spoon a little of the bean cooking liquid into the side of the gratin, to avoid wetting the breadcrumbs.
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