1. A method of multiphase deduplication, the method comprising: a backup phase that includes storing, in a deduplication vault storage, a backup of a source storage, the backup including each unique nonduplicate allocated block from the source storage at a point in time including file system metadata (FSM) blocks and data blocks; a virtual defragmentation phase that includes accessing the FSM blocks included in the backup and reordering block references in the FSM blocks to match the order of the corresponding blocks as stored in the deduplication vault storage; and a restore phase that is performed after the completion of the virtual defragmentation phase and that includes reading, from the deduplication vault storage, and storing, in a restore storage, each allocated block that was stored in the source storage at the point in time according to the reordered block references in the FSM blocks.