When adding nuts, dried fruits, herbs, cheese, and things of that nature then you can wait and add those when you get to the shaping of the loaves. This makes it simple to change up the recipe per loaf and try a ton of flavor combos with less batches of dough! If you are getting into variations that involve different types and styles of grain/flour then you'll need to make those adjustments as you mix your ingredients for the dough. Have fun experimenting Nick! 

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