The Midwife's Apprentice is set in medieval England, and the realities of life in a small English village during that period of time contribute to the mood and tone of the story in many ways. Even in the first few sentences, a fact of life in medieval England sets the tone:
When animal droppings and garbage and spoiled straw are piled in a great heap, the rotting and moiling give forth heat. Usually no one gets close enough to notice because of the stench. But the girl noticed, and on that frosty night, burrowed deep into the warm, rotting muck, heedless of the smell.
Medieval England lacked many of the services we take for granted in modern times, such as regular garbage pickup and disposal. During medieval times, there also weren't laws against littering. Because of this, it wasn't unusual for the streets to be full of garbage and other nasty stuff.
But what does this have to do with the mood or tone of the story? Well, Karen Cushman, the author of The Midwife's Apprentice, takes advantage of this "feature" of medieval life to set up a fairly grim mood (this isn't a nice, pretty, perfume-filled place we're reading about).
At the same time, Cushman doesn't use a sad or shocked tone. Instead, she uses a very matter-of-fact, straightforward tone. This makes it clear that the garbage wasn't unusual at all—it was just a fact of life that people were used to.