Coat the eggplant and squash pieces with your hands in 2 tablespoons of flour and set aside.
Heat 2 tablespoons of olive oil in the skillet and add the chopped garlic and the chopped onions. Cook on medium heat, stirring occasionally for 3 – 5 minutes, until the onion is transparent.
Add the chopped peppers. Cook at medium heat 4-6 minutes longer, stirring occasionally, until the peppers have softened. Remove the vegetables from the pan and set aside.
Raise the heat to medium-high and add the remaining 3 tablespoons of olive oil. Once the oil is hot add the squash and eggplant. Cook for approximately 5 minutes, stirring to prevent the flour from burning and to cook all sides of the cubes. Some flour may stick to the pan but the next step will allow you to stir it back into the stew with the wooden spoon.
Add the peppers, onion, and garlic back into the pan. Sprinkle the thyme and lightly salt and pepper the mixture. Cover (with a tight lid) and cook under a medium-low heat for about 10 minutes, stirring occasionally. The squash and eggplant need to “sweat” and the water recirculate back into the stew.
Uncover and raise the heat to medium. Add the canned tomatoes, and their juice, simmer and cook for 25-30 minutes at a low simmer. Add salt and pepper. (The flavor of the ratatouille will intensify if refrigerated and served the next day)
Serve with a tossed salad, crusty bread or cheese
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