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To make the topping: Prepare the Simple Berry Jam (recipe follows).
To Make the Crust: Position a rack in the center of the oven. Preheat the oven to 450ºF/ 230ºC. Grease a 9-inch/23-cm springform pan.
In a medium bowl, mix together the cracker crumbs, butter, sugar, vanilla, and salt. Press the mixture into the bottom of the pan, using your hands or the flat bottom of a small measuring cup to compress the crust. Put the pan in the freezer.
To Make the Filling & Topping: In a large bowl using a handheld mixer (I find this works best for the job, rather than a stand mixer), beat the cream cheese, sugar, flour, lemon zest, and orange zest on medium speed for 3–5 minutes, stopping the mixer and scraping down the sides of the bowl and the beaters to make sure there’s no lumpy cream cheese in sight. With the mixture on its lowest speed, add the eggs, egg yolks, and vanilla all at once, mixing until smooth and the eggs are well incorporated. Mix in the sour cream until just incorporated.
Remove the Crust from the freezer, put on a rimmed baking sheet, and wrap the sides of the pan with aluminum foil. Pour the filling into the prepared pan and put the pan on a baking sheet. Bake for 17–20 minutes, until the top is puffed.
Lower the oven temperature to 225ºF/110ºC and bake until the cake is mostly firm but still slightly wobbly in the center, 45 minutes to 1 hour more. (If the cheesecake is not done after 45 minutes, check it every 5 minutes or so until it is—it seems like a daunting task, but cheesecake-making requires a bit of saintly patience.)
Once the cheesecake is done, remove it from the oven and allow it to cool to room temperature in the pan. Cover and refrigerate it for 8 hours before topping.
In a small saucepan over medium heat, combine the jam with 1 teaspoon water until it is pourable. Let it cool to room temperature and pour over the cheesecake. Return the cheesecake to the refrigerator until the jam topping is set before serving and topping with the fresh berries. The cheesecake will keep, covered, in the refrigerator for up to 5 days; be sure to top the cheesecake with the fresh berries no longer than a day in advance of serving.