Preheat the oven to 300 degrees F.
For the crust: In a medium bowl, combine the cracker crumbs and sugar. Add the melted butter, stirring to combine. Press the crust into the bottom and 1 inch up the sides of a 9-inch springform pan. Bake for 6 minutes; let cool.
For the chocolate layer: Using a double boiler, melt the chocolate and butter (or microwave on high in 30-second intervals, stirring after each, until the chocolate is melted and smooth, about 1 1/2 minutes total). Whisk in the sugar, eggs, and flour until just combined. Pour into the bottom of the cooled crust and bake for 15 minutes; let cool.
For the cheesecake layer: Spread the caramel topping evenly over the cooled chocolate layer. Cut the cookie dough crosswise into 1-inch slices. Place the slices in an even layer over the caramel, pressing gently together to seal the edges.
In a large bowl, beat the cream cheese and sugar on medium speed with an electric mixer until creamy. Beat in the eggs, 1 at a time, beating well after each addition. Beat in the vanilla and flour until just combined. Stir in the sour cream. Pour the mixture over the cookie dough layer and bake until the cake is cracked and browned around the edge, about 1 hour. Remove from the oven and gently run a knife around the edges to release the crust from the sides of the pan. Let cool completely.
For the ganache: Using a double boiler, combine the chocolate and cream and melt (or microwave on high in 30-second intervals, stirring after each, until the chocolate is melted and smooth, about 1 minute total). Spread over the cooled cheesecake. Refrigerate for at least 8 hours before serving.
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