1. A method of deduplicating data performed by one or more computing systems, each computing system having a processor and memory, the method comprising: receiving an indication of a first storage operation; creating a first directory associated with the first storage operation, wherein the first directory includes three files, wherein the first file of the first directory stores data associated with the first storage operation, and wherein the data in the first file is de-duplicated, wherein the second file of the first directory stores data associated with the first storage operation, and wherein the data in the second file is not de-duplicated, wherein the third file of the first directory stores a first data structure that includes information identifying file locations of data within the first file corresponding to data in the second file, and wherein the data stored in the first and second files of the first directory is not tracked by file systems of the one or more computing systems; receiving a first set of multiple, discrete data objects associated with the first storage operation, wherein each of the multiple data objects of the first set include a header portion and a payload portion; determining, by the one or more computing systems, that the payload portion of a first data object of the first set has already been stored in the first file of the first directory, and updating the first data structure to track the location of the payload portion of the first data object; storing the header portion of the first data object in the second file of the first directory; and determining, by the one or more computing systems, that the payload portion of a second data object of the first set has not already been stored in the first file of the first directory, and both storing the payload portion of the second data object in the first file of the first directory and updating the first data structure to track the location of the payload portion of the second data object; and storing the header portion of the second data object in the second file of the first directory.