Dependently typed languages such as Agda, Coq, and Idris use a syntactic first-order unification algorithm to check definitions by dependent pattern matching. However, standard unification algorithms implicitly rely on principles such as uniqueness of identity proofs and injectivity of type constructors. These principles are inadmissible in many type theories, particularly in the new and promising branch known as homotopy type theory. As a result, programs and proofs in these new theories cannot make use of dependent pattern matching or other techniques relying on unification, and are as a result much harder to write, modify, and understand. This paper proposes a proof-relevant framework for reasoning formally about unification in a dependently typed setting. In this framework, unification rules compute not just a unifier but also a corresponding soundness proof in the form of an equivalence between two sets of equations. By rephrasing the standard unification rules in a proof-relevant manner, they are guaranteed to preserve soundness of the theory. In addition, it enables us to safely add new rules that can exploit the dependencies between the types of equations, such as rules for eta-equality of record types and higher dimensional unification rules for solving equations between equality proofs. Using our framework, we implemented a complete overhaul of the unification algorithm used by Agda. As a result, we were able to replace previous ad-hoc restrictions with formally verified unification rules, fixing a substantial number of bugs in the process. In the future, we may also want to integrate new principles with pattern matching, for example, the higher inductive types introduced by homotopy type theory. Our framework also provides a solid basis for such extensions to be built on.