Preheat oven to 425°F. In a bowl, toss tomatoes, eggplant, fennel seeds, and red pepper flakes with olive oil and sea salt; then, pour onto a parchment paper lined baking sheet and bake for 30 minutes. Remove and let cool.
Heat olive oil in a Dutch oven. Add green beans, tossing every minute until tender crisp. Add garlic, wine, and tomato paste. Mix well and add ¾ cup water, tomatoes and butter beans. Re-cover the pot and cook until tomatoes start to burst. Remove pot from heat and stir in oregano and thyme.
Spread Gruyere out on a parchment-lined baking sheet and bake until bubbling and golden. Let cool.
Place roasted tomatoes, eggplant, and tomato bean mixture on a serving platter and garnish with Gruyere crisps.