Step 1Place the eggplant in a colander. Toss with 1/2 teaspoon of salt. Let rest for 30 minutes. Rinse well with cold water, shaking the colander to remove as much water as possible.
Step 2Heat the olive oil in a large skillet or Dutch oven over medium-high heat. Add the onions, celery, garlic and red pepper flakes. Cook, stirring often, until the onions are softened but not browned, about 5 minutes.
Step 3Add the rinsed eggplant, zucchini, bell pepper, thyme, 1 tablespoon of salt, the basil and oregano. Cook, stirring often, until heated through, about 5 minutes. Add the tomatoes and juice, vinegar and honey. Stir well. Simmer, uncovered, until the eggplant is just tender but keeps its shape and is not soft or mushy, about 5 to 7 minutes more. Taste; season to taste with pepper and salt. Stir in the pine nuts, if using.