1. A method for managing an organization of data, the method comprising: generating a candidate reference taxonomy for representing an organization of stored data for multiple disparate application programs that are operating under different operating systems in different computer systems, wherein the candidate reference taxonomy is a proposed hierarchical organization of folders for the stored data; comparing the candidate reference taxonomy with an application taxonomy for each of the multiple disparate application programs wherein an application taxonomy is an innate hierarchy of folders that is associated with a particular application program; and in response to a user selecting the candidate reference taxonomy to be used to replace the application taxonomies for the disparate application programs, storing the candidate reference taxonomy as a replacement reference taxonomy for the application taxonomies for all of the disparate application programs, wherein each of the disparate application programs utilizes the replacement reference taxonomy instead of an application taxonomy to organize the folders of the stored data, and wherein the replacement reference taxonomy generated from an aggregation of data structures and data interrelationships used by two or more of the multiple disparate application programs repositions depictions of folders found in the innate hierarchy of folders that was associated with the particular application program.