Preheat the oven to 350F°/176°C. Chop the bread into ¾-inch (2 cm) cubes and transfer to a rimmed baking sheet. Drizzle 1 ½ tablespoons of extra virgin olive oil and lightly sprinkle with salt, and toss to coat. Bake in the oven for 10 minutes, until lightly golden but not too hard.
Meanwhile, in a very large bowl (the largest bowl you have), combine the tomatoes, and shallots. Separate the shallots into individual rings as much as possible. Add the garlic, thyme leaves, and beans. Drizzle the mixture with 2 tablespoons of extra virgin olive oil and season with 1 ½ teaspoons of kosher salt and lots of freshly cracked black pepper. Toss well to combine.
Add the baked bread cubes to the mix and gently toss to ensure the bread cubes are coated and well combined. Transfer the tomato mixture to a 3-quart/3-liter baking dish (I used a 13x9" pan).NOTE: if your bowl isn’t big enough to hold the bread cubes, transfer the tomato-shallot mixture to the baking dish, then mix in the bread.
Bake the casserole in the preheated oven at 350°F/176°C for 35 to 40 minutes, until the top bread pieces are golden and crunchy.
Meanwhile, make the Cashew Parmesan. Add the cashews, nutritional yeast, 1/2 teaspoon kosher salt, and 1/2 teaspoon extra virgin olive oil to a food processor. Pulse repeatedly in 1 second bursts until the mixture has a fine, crumbly texture, somewhat similar to grated parmesan (do not continuously blend, or you’ll end up with cashew butter).
Meanwhile, make the Caper Gremolata. Finely chop the parsley and basil together. Using a microplane, grate the garlic directly over the parsley and basil (or mince the garlic with a knife). Add the capers on top, and chop everything together until well combined. Sprinkle with a bit of flaky or coarse sea salt.
Remove the casserole pan from the oven. Using oven mitts, arrange an oven rack for the broiler (but don't position it too close to the flame) and set your broiler to a low heat.
Sprinkle a generous layer of Cashew Parmesan on top of the baked dish and put it under the broiler for a couple minutes until the topping is nicely browned, but keep an eye on it to prevent burning. NOTE: For reference, my maximum broiler temperature is 550°F/288°C, so I set it to 500F/260°C and broiled for about 60 to 90 seconds, then reduced the heat to 475°F/245°C and broiled for another 30 to 60 seconds.
Allow the casserole to cool for 10 minutes, then evenly sprinkle the top with the Caper Gremolata. Finish the casserole with a few drizzles of extra virgin olive oil and a light sprinkle of flaky or coarse sea salt.