For dough: Pulse flour and salt in a food processor. Add butter and pulse about 10 times until mixture resembles a coarse meal. Add egg and pulse 1 to 2 times more into a rough dough. Remove and gently press into a disk. Wrap tightly and refrigerate for 1 hour or up to 2 days.
Preheat over to 400 degrees F.
For filling: Slice apple, squash, and onion into 1/2-inch thick slices. Place in a large bowl and toss with melted butter, rosemary, and thyme. Season with salt and pepper, to taste.
Roll dough on a lightly floured surface into a 12-inch circle. Transfer to a baking sheet and brush with mustard. Leaving a 2-inch border from edge, arrange apple, squash, and onion slices over dough in an overlapping circle. Fold border over edge of filling, pleating as needed to make a free form pie. Bake until crust is brown and apple, squash, and onion are tender and brown, about 55 minutes. Scatter cheese over filling and bake until melted, about 5 minutes more. Transfer to a wire rack and cool slightly. Cut into wedges and serve.
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