What does "combine dry ingredients through cloves" mean?
It means to combine the things listed up to and including the cloves, as in "combine ingredients 4 through 11". In that recipe it's just a helpful hint to tell you where the dry ingredients stop.

The recipe is already calling for ground cloves - it mixes them into dry ingredients as-is. When using whole cloves, if you don't immediately just grind them, you generally cook them in something liquid then strain them out later. (Similar to cinnamon sticks or whole allspice.) The cinnamon and nutmeg in the recipe are also ground, not whole. If a recipe wants whole cloves, it will explicitly say, and often count them: 10 [whole] cloves.