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There's no configuration file (patches welcome!). There are some tunables hardcoded in the source that could eventually become configuration options. There's also an incomplete option parser (patches welcome!).
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The bees process doesn't fork and writes its log to stdout/stderr. A shell wrapper is required to make it behave more like a daemon.
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There's no facility to exclude any part of a filesystem or focus on specific files (patches welcome).
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PREALLOC extents and extents containing blocks filled with zeros will be replaced by holes. There is no way to turn this off.
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Consecutive runs of duplicate blocks that are less than 12K in length can take 30% of the processing time while saving only 3% of the disk space. There should be an option to just not bother with those, but it's complicated by the btrfs requirement to always dedupe complete extents.
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There is a lot of duplicate reading of blocks in snapshots. bees will scan all snapshots at close to the same time to try to get better performance by caching, but really fixing this requires rewriting the crawler to scan the btrfs extent tree directly instead of the subvol FS trees.
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Block reads are currently more allocation- and CPU-intensive than they should be, especially for filesystems on SSD where the IO overhead is much smaller. This is a problem for CPU-power-constrained environments (e.g. laptops running from battery, or ARM devices with slow CPU).
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bees can currently fragment extents when required to remove duplicate blocks, but has no defragmentation capability yet. When possible, bees will attempt to work with existing extent boundaries, but it will not aggregate blocks together from multiple extents to create larger ones.
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When bees fragments an extent, the copied data is compressed. There is currently no way (other than by modifying the source) to select a compression method or not compress the data (patches welcome!).
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It is theoretically possible to resize the hash table without starting over with a new full-filesystem scan; however, this feature has not been implemented yet.