1. A method of generating a backup data set for a client computing device by using a signature repository residing in a primary storage subsystem, the method comprising: for each respective client computing device of one or more client computing devices in a primary storage subsystem: monitoring the storage of a plurality of files formed by data blocks generated by one or more software applications running on the respective client computing device, wherein the plurality of files are stored in a data store associated with the respective client computing device; maintaining, by a repository agent executing on one or more processors in the primary storage subsystem, a repository indicating at least which data blocks of the monitored files are stored in the primary storage subsystem; in response to instructions to create a secondary copy in a secondary storage subsystem of at least a subset of the plurality of files stored in a data store associated with a first client computing device of the one or more client computing devices, querying the repository to identify at least a first group of data blocks that form at least a portion of the subset of files and for which matching data blocks are not stored in the secondary storage subsystem; identifying the location of the first group of data blocks within the primary storage subsystem; and retrieving the first group of data blocks from one or more of the data stores associated with the one or more client computing devices.