When converting a recipe for bakers percent, is the hydration % related only to the flour weight ? For instance if I have a recipe that contains other dry goods such as wheat germ or potato flakes along with flour, is the hydration % based on the total weight of the flour, or do I take into account the other dry goods combined with the flour ?
I have seen the matter you raise handled in different ways. For example, I have seen spreadsheets for bread dough where each flour ingredient in a multi-flour blend is listed separately and where the hydration is calculated with respect to the total blend. On this forum, many of our members use the dough calculating tools at http://www.pizzamaking.com/dough_tools.html.
However, those tools were not specifically designed to do hydration calculations when the "flour" includes several components. In those cases, the "flour" is really a blend. The blend might comprise two or more flours, such as a high-gluten flour and a 00 flour, or it might include a base flour, like an all-purpose or bread flour, and things like wheat germ, vital wheat gluten (VWG), and semolina. You can see how I handle those three specific situations at:
Reply 283 at http://www.pizzamaking.com/forum/index.php/topic,3940.msg155934/topicseen.html#msg155934
Reply 52 at http://www.pizzamaking.com/forum/index.php/topic,6758.msg66312.html#msg66312
Reply 79 at http://www.pizzamaking.com/forum/index.php/topic,8167.msg71404/topicseen.html#msg71404
By treating flours and flour blends alike from the standpoint of hydration calculations, the rest of the ingredient quantities will also be based on the flour or flour blend. Otherwise, the quantities of those other ingredients will be off.
An additional important point to keep in mind is that when you modify an existing recipe or formulation to add something else to it, such as eggs, honey, beer, milk, dry milk powder, potato flakes/powders, or other wet or dry ingredients, especially in large quantities, it becomes necessary to adjust the formula hydration to compensate for the wetness or dryness that those ingredients contribute to the dough. That usually means researching the additional ingredients to determine their moisture content and making the necessary adjustments based on those moisture contents.