Preheat oven to 350 degrees, with racks in upper and lower thirds. In a medium bowl, whisk together flours, baking soda, nutmeg, salt, and pinch of cloves. In a large bowl, using an electric mixer, beat butter and brown sugar on high, scraping down bowl as needed, until light and fluffy, about 4 minutes. Beat in eggs, one at a time, scraping down bowl after each addition. With mixer on low, beat in half the flour mixture, then milk and remaining flour mixture. Beat just until combined.
With a rubber spatula, fold apples and raisins into dough. Drop dough in 2-tablespoonful mounds, 2 inches apart, onto two baking sheets. Bake until cookies are firm around edges, about 14 minutes, rotating sheets halfway through. Let cool completely on wire racks.
In a small bowl, whisk together confectioners' sugar and 1 tablespoon water. Transfer to a zip-top bag. Snip a very small hole in one corner and drizzle glaze over cookies.
These cookies can be made up to 5 days ahead and stored in an airtight container at room temperature. To keep them looking pretty, glaze them just before serving.