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Combine the water and 1 1/2 tablespoons salt in a large mixing bowl and stir to dissolve the salt. Add the beans, cover the bowl, and let stand at least 6 hours or overnight.
Preheat the oven to 325°F.
In a heavy stock pot or Dutch oven over medium heat, cook the bacon. Once all the fat has rendered, remove the bacon with a slotted spoon and drain on a paper towel-lined plate. Pour off all put one tablespoon of bacon fat. Cook the onions slowly with 1/2 teaspoon of salt start to caramelize and turn golden brown, 15 to 20 minutes. Add the celery and cook just until the celery is softened, about 3 minutes. Add the garlic and cook until fragrant, about 30 seconds.
Remove half of the onion mixture and reserve with the bacon. Deglaze the pan with one cup of wine or water, scraping up any brown residue that has formed on the bottom of the pan.
Drain and rinse the beans and pour them into the pot with the remaining onions. Add the bay leaf, 1 teaspoon of salt, and enough water to cover the beans and onions by 1 inch. Cover the pot and transfer to the oven. Cook for 1 hour, then begin checking the beans for doneness. Check the beans every 15 minutes until they are completely soft and creamy. (This can take up to 2 1/2 hours depending on the age and exact variety of your beans.)
→ Make-Ahead Tip: At this point, the soup can be chilled and refrigerated for a day or two before serving. The soup (or a portion of it) can also be frozen for up to three months.
Set the pot of cooked beans over medium-high heat on the stovetop. Add the bacon, reserved onions, thyme, pasta, and 1 teaspoon of salt. Cook, stirring occasionally, until the pasta is al dente. Add more water if necessary so the pasta is submerged.
Add the spinach to the pot and stir until it is wilted. Remove the bay leaf and the thyme stems. Taste and add more salt and pepper if desired.