Spread the dry beans out on a flat surface and remove any rocks or debris. Rinse the beans well, then drain. Place the beans in a large pot and cover them with fresh filtered water, ensuring the water level is about 3 inches above the beans. Cover and allow the beans to soak overnight or for at least 8 hours. The beans should visibly double in size.

Heat 1 tablespoon of oil in a large pot or Dutch oven over medium-low heat. Swirl the oil to coat the bottom of the pot. Add the halved lemon and onions, cut side down, and cook undisturbed. After 3 minutes, add the garlic halves, cut side down, and cook undisturbed for an additional 3 minutes, or until the onions, lemons, and garlic are slightly charred on the bottoms. Add the remaining tablespoon of oil and red pepper flakes, allowing to cook for 1 minute.

Drain and rinse the soaked beans, then add them to the pot along with the rosemary, thyme, bay leaves, and 8 cups of filtered water to submerge the beans. Bring to a boil, then reduce heat to a gentle simmer. Partially cover the pot and cook for about 30 minutes.

Add the salt and stir the beans well. Partially cover the pot again and cook for an additional 1 to 1 ½ hours. During this time, check the beans about every 30 minutes, stirring briefly and adding more water if the beans are no longer fully submerged.

Test a few beans to ensure they are tender and fully cooked. Squeeze the garlic out of its skin directly into the pot along with the juice from the lemon. Discard the garlic skins, lemon, onions, rosemary and thyme sprigs, and bay leaves.

For added umami flavor, transfer a ladleful of broth to a large mug and whisk in the miso paste until fully dissolved. Pour the mixture back into the pot of beans, stirring well. Taste the broth and adjust the salt to your preference.

To make the salsa, combine the avocado, scallions, parsley, jalapeño, lemon zest and juice, and a pinch of salt in a mixing bowl. Stir well to combine.

To serve, spoon the brothy beans into a serving dish and top with a few spoons of the avocado salsa. Finish with a few cracks of black pepper and enjoy with toasted bread!