What was the main conflict in The Boy in the Striped Pajamas?

The main conflict in the novel is one of friendship. 
Particularly, the conflict resides in how friendship can transcend the conditions of
circumstances and contingency.  The loyalty shared by Bruno and Shmuel is a transcendent
one.  It is one based on the ethos of care, compassion, and expansion of moral
imagination to fully grasp the plight of another.  It is this very essence that is
challenged by the circumstances of the Nazis and the Holocaust.  The conflict present is
what happens to values that represent permanence in a condition that emphasized
contingency and impermanence.  This conflict is what plays out between the two boys,
enabling Bruno to understand the plight of his friend, change into "pajamas" in helping
his friend find his father, and ultimately allows them to walk hand in hand into a
situation where transcendence might have been wounded, but certainly not
wounded.