Heat the butter in a medium saucepan over medium-high heat. Add the shallot, apples, and thyme; saute until tender, about 3 minutes. Add the raisins, cranberries, lemon zest and juice, orange juice, and sugar. Reduce the heat to a low simmer and cook, stirring occasionally, until the mixture has thickened, about 20 minutes. Remove from the heat and let cool. Transfer to a serving bowl and serve.