Representations of hierarchical structures identified by source and target file storage directories are displayed on a display device. Inconsistencies are identified between the hierarchical structures identified by the source and target file storage directories. Graphical interconnections are displayed that extend at least partially between locations of at least some of the identified inconsistencies. Refactoring action indicia are displayed that are user selectable and are associated with defined actions performed by a file directory controller to modify the hierarchical structure identified by the target file storage directory to resolve at least some of the inconsistencies identified between the hierarchical structures identified by the source and target file storage directories. The source and target file storage directories are merged, including by performing the defined actions associated with user selected ones of the refactoring action indicia to generate a refactored target file storage directory that resolves the inconsistencies.