In a medium bowl, whisk together the flour, wheat germ, baking powder, baking soda, salt, cinnamon, nutmeg, cloves, and ginger. In a large bowl, beat the butter with an electric mixer set on high speed until creamy, about 1 minute. Gradually beat in the granulated and brown sugars and beat until light and fluffy, about 2 minutes. One at a time, beat in the eggs, followed by the vanilla, scraping down the sides of the bowl as needed. Add the pumpkin and beat until combined. Add the apples and walnuts. With the mixer set on low speed, min in the flour mixture in thirds, scraping down the bowl as needed. Spread the batter in the prepared pan.