Heat 2 tablespoons of the olive oil in a pan and cook the onions over a medium heat, shaking the pan frequently, until browned. Add a splash of water and reduce the heat to very low. Cover and sweat for a further 10 minutes, or until soft.
Meanwhile, heat 2 tablespoons of the olive oil in a frying pan and add the kale and garlic. Stir-fry over a medium–high heat until the kale is tender, about 1 minute. Set aside.
Heat the oven to 190°C (375°F/Gas 5). Warm the cheese sauce, adding a splash of wine or a little water to achieve the consistency of double cream. In a large mixing bowl, gently combine the cheese sauce, onions, kale, beans, thyme, lemon zest and salt and pepper. Taste for seasoning: beans need lots of salt. Transfer to a lightly oiled ovenproof dish measuring 25 x 18 cm (10 x 7 inches) or similar.
Blitz the ciabatta or sourdough in a blender or food processor to crumbs. Add the nutritional yeast and remaining olive oil and pulse to combine. Sprinkle the crumbs over the creamy vegetables to completely cover. Cook for 25–30 minutes until the top is golden and the sauce bubbling. Serve immediately.