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Step 1
Arrange an oven rack in the middle position and preheat the oven to 375 degrees F.
Step 2
In a 12-inch cast-iron pan over medium heat, add the oil and 2 tablespoons of butter. When the butter is melted, add the carrots, celery and onions and season with 1/2 teaspoon kosher salt. Cook, stirring occasionally, until the onions are softened, about 7 minutes. Add the thyme, za'atar, paprika, cayenne and garlic and cook until sizzling, about 30 seconds. Add the red wine. Bring to a boil and then lower to a simmer to reduce by half, 1 to 2 minutes. Add the broth and tomatoes and bring to a simmer. Simmer for 5 minutes. Add the chickpeas, parsley, butternut squash, apple and bay leaf and bring back to a simmer. Simmer for 10 to 15 minutes, until the vegetables are tender and the sauce is thickened.
Step 3
Add the vinegar and honey and season with 1 teaspoon kosher salt. Remove from the heat.
Step 4
Lay the phyllo on your work surface. Brush 1 sheet with some of the melted butter and sprinkle with a little za'atar. Slide your hands under the sheet and loosely crumple it from underneath; it should sort of look like a messy rose. Lay on top of the pot pie. Repeat with the remaining phyllo and butter, sprinkling each with a little za'atar. Sprinkle all over with a little flaky salt. Bake until the phyllo is crisp and golden and the vegetables are tender, 25 to 30 minutes. Sprinkle with a little more parsley and serve.
Step 5
Let leftover pot pie come to room temperature and then store, phyllo on top, in a covered container in the fridge for up to 2 days.