Drain the pre-soaked beans and combine them with the water in a large pot.
Stick the whole cloves into the onion and throw it into the pot with the beans along with the thyme and bay leaves. Cover and bring to a boil. Simmer, partially covered, until the beans are tender, 1 to 1 1/2 hours depending on the type and the age of the beans. Skim off any foam that rises to the top during the cooking process.
Meanwhile, heat the oil in a frying pan and add the sliced garlic. Cook over medium heat, stirring, until the garlic is soft and has taken on a bit of color, but be careful not to burn it or it will go bitter. Remove from heat and mash with a fork.
When the beans are done remove the onion and bay leaves and discard; then add the roasted garlic, chili flakes and the kale. Cook for another 5-ish minutes until the kale softens. Season to taste with a generous amount of salt and pepper and stir in the nutritional yeast. Serve with crusty sourdough bread and additional chili on the side.