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In backup systems, the chunks of each backup are physically scattered after deduplication, which causes a challenging fragmentation problem. We observe that the fragmentation comes into sparse and out-of-order containers. The sparse container decreases restore performance and garbage collection efficiency, while the out-of-order container decreases restore performance if the restore cache is small. In order to reduce the fragmentation, we propose History-Aware Rewriting algorithm (HAR) and Cache-Aware Filter (CAF). HAR exploits historical information in backup systems to accurately identify and reduce sparse containers, and CAF exploits restore cache knowledge to identify the out-of-order containers that hurt restore performance. CAF efficiently complements HAR in datasets where out-of-order containers are dominant. To reduce the metadata overhead of the garbage collection, we further propose a Container-Marker Algorithm (CMA) to identify valid containers instead of valid chunks. Our extensive experimental results from real-world datasets show HAR significantly improves the restore performance by 2.84-175.36 $\times$ at a cost of only rewriting 0.5-2.03 percent data. [ABSTRACT FROM PUBLISHER]