A system and method for storing data. In one embodiment, a file system includes a hierarchy of nodes partitioned into a plurality of containers. The file system further includes metadata associated with each node. First metadata describes each node's references to other nodes and second metadata identifies each node's parent node. The file system further includes a linkage table associated with each container. Each linkage table comprises entries describing links between a node owned by the associated container and other nodes. In response to detecting that a file system error has occurred, the file system identifies a container which corresponds to the detected error, corrects inconsistencies between the first and second metadata associated with each node owned by the container, and corrects inconsistencies between each of the entries of the linkage table associated with the identified container and the first and second metadata.