How was the conflict in The Boy with the Striped Pajamas resolved?

The conflict at the heart of the story is a culture clash between the two different worlds that Bruno and Shmuel occupy. Though physically separated by nothing more than a fence, the two boys might as well live on different planets. Bruno is a German; his father, the commandant of Auschwitz, plays a key role in the Nazi genocide against the Jews. Shmuel is himself a Jew, a victim of the campaign of terror and physical annihilation waged against his people by the Nazis.
It seems scarcely believable that two boys from such radically different backgrounds should be able to forge any kind of meaningful friendship. That they do so is a testament to the power of humanity to transcend the artificial racial and ethnic barriers that people construct to keep themselves separate.
And it is this unique friendship that ultimately resolves the book's central conflict, albeit tragically. For it is only when Bruno goes with Shmuel to die in Auschwitz's notorious gas chambers that the divisions between them finally collapse. That it takes their deaths to resolve this conflict speaks volumes about the world that Bruno's father has helped to create.

The main conflict throughout the novel involves the circumstances surrounding Bruno and Shmuel's friendship. Since Bruno is the son of a Nazi Commandant and Shmuel is a Jewish prisoner, their friendship is forbidden. Bruno and Shmuel are forced to meet in secret and talk between the fence that separates them. Despite the fact that they cannot play together and are forbidden from interacting, Bruno and Shmuel develop a strong friendship. Shmuel listens to Bruno, and Bruno brings Shmuel food each trip. Bruno eventually agrees to help Shmuel find his father and crawls underneath the fence. Unfortunately, the boys are forced to march with a group of Jewish prisoners to a gas chamber. Although the two boys die, the conflict is resolved because their friendship and loyalty transcend their terrible environment. At Auschwitz, the boys' friendship was forbidden, but in death, they are given the chance to be together for eternity.