Heat 3 tablespoons of olive oil in a 6 quart or larger Dutch oven over medium-high heat. Add the onions, leek, carrots, celery, zucchini, and squash. Sauté for 5 minutes. Veggies should be lightly browned
Add the garlic, red pepper flakes, thyme, and rosemary. Cook about 1 minute
Stir in the broth, beans, and tomatoes. Bring the contents to a boil, then turn the heat down to low.
Simmer for 20 minutes. Add the chopped kale. Cover the pot and simmer for 20 minutes.
Use an immersion/stick blender to partially puree the soup, leave some chunks of beans vegetables for texture. Add the salt, pepper, and vinegar. Taste and adjust seasonings as needed.