In a saucepan, toast the fennel, mustard and cumin seeds over moderate heat until fragrant, 1 minute. Transfer to a plate; let cool.
In the same saucepan, cook the tomatoes with the granulated and brown sugars over moderate heat, stirring, until the sugars dissolve. Add the garlic, ginger and toasted seeds and simmer over moderate heat, stirring, until the chutney is thick and reduced to 2 1/2 cups, 15 minutes. Stir in the jalapeño; transfer to a bowl to cool. Season with salt and cayenne. Refrigerate overnight before serving at room temperature.
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