Adding inclusions like vegetables, fruits, nuts, and meats to bread loaves and rolls is usually done either during the initial mixing stage or during shaping. When you should add the inclusions really depends on how large the ingredients are and how you want them distributed in the final loaf. When adding inclusions at the initial mix it is advisable to add them late in the mix/knead, after some gluten development has already occurred. Adding them early in the mix can increase your kneading time, break up or pulverize your inclusion, or give an uneven or "off" color to the crumb from juices and colors bleeding out of the included ingredient.
Smaller, minced, or chopped inclusions can be added during the mix if you want it distributed evenly
or at shaping if you want it to appear in a distinct layer. Larger inclusions are easier to add during shaping.
Inclusions with high water (like fresh tomatoes) or fat content (like raw bacon or pepperoni) will cause large cavity formation and layer separation that might make it difficult to use the bread as a base for sandwiches and can lead to doughy undercooked areas around the inclusion. To reduce this effect you can use a drier/dried version of fruits and vegetables such as dried tomatoes or raisins; you should render out the fat from bacon or pepperoni by pre-cooking. If you pre-cook your bacon or pepperoni before you mix the other ingredients you can add some of the rendered fat to the mix so that the flavor permeates the bread, just reduce the amount of butter or oil called for in your original recipe.
Cheese can be added at either stage and can cause issues related to both water and fat if the wrong type of cheese is used. Cheeses that tend to release oil and separate (like Cheddar and most aged cheeses) are better grated and added in the initial mix. Cheeses (like Jack, Colby, Havarti, or American) that melt well can be added grated at either stage.
Most inclusions have little noticeable effect on leavening. Cured meats and cheeses contain salt so you may need to reduce the total salt added to the dough; the curing salts used in cured meats may slightly reduce yeast activity. Spices like cinnamon, cardamom, ginger and nutmeg can increase yeast activity, while mustard inhibits yeast activity.
Other Tips on Bread Inclusions