We initiate the theoretical study of directory reconciliation, a generalization of document exchange, in which Alice and Bob each have different versions of a set of documents that they wish to synchronize. This problem is designed to capture the setting of synchronizing different versions of file directories, while allowing for changes of file names and locations without significant expense. We present protocols for efficiently solving directory reconciliation based on a reduction to document exchange under edit distance with block moves, as well as protocols combining techniques for reconciling sets of sets with document exchange protocols. Along the way, we develop a new protocol for document exchange under edit distance with block moves inspired by noisy binary search in graphs, which uses only $O(k \log n)$ bits of communication at the expense of $O(k \log n)$ rounds of communication.