Methods and systems are provided for reconciling any changes that have occurred in two file trees since they were last synchronized. A reconciler takes as input two logs of the changes made in the respective file trees. The first log resides on a client computing device, and the second log resides on a server computing device. The reconciler outputs two sets of changes that need to be applied to the respective file trees in order to synchronize them. The reconciler detects and outputs a list of changes that conflict with each other.