Step 1Chop the bacon into rough squares. Combine with the onion, 1 crushed garlic clove, the beans, water and salt in a heavy pan. Bring to a simmer, then cook, tightly covered, over low heat until the beans are tender, 2 to 2 1/2 hours. Check occasionally; if the beans begin to go dry, add a little more water.
Step 2When the beans are quite tender, remove from the heat, add the tomatoes and sage and stir very roughly to crush some of the beans (their starch will thicken the liquid).
Step 3While the beans are cooking, peel the squash, cut it in half and scoop out the seeds. Cut the flesh into one-half-inch dice. Steam the squash over rapidly boiling water until tender, about 7 to 10 minutes. Remove from the steamer and cool slightly before stirring (so cubes retain their shape).
Step 4Remove the crust from the baguette and coarsely chop the bread. Place it in a blender or food processor with the remaining garlic clove and grind to coarse crumbs.
Step 5Heat the oven to 400 degrees. Generously brush a 3- to 3 1/2 -quart gratin dish with 2 teaspoons olive oil. Spoon the squash cubes into the dish, being careful not to crush them. Using a slotted spoon, ladle the cooked beans over the top. Add just enough of the bean liquid to cover the bottom of the dish. Stir lightly to combine.
Step 6Spoon the garlicky bread crumbs over the top, covering the dish in a thick mound. Drizzle with olive oil. Bake until the bread crumbs are deep brown (you will notice the fragrance turning from overtly garlicky to something more complex and beany), about 40 minutes. Remove the pan from the oven and let stand 5 minutes before serving.