https://btrfs.wiki.kernel.org/index.php/Deduplication : bedup implements incremental offline whole-file deduplication for Btrfs. It works on mainline kernels (Linux 3.3 is required by the file locking implementation, 3.6 is required for cross-subvolume operation), using the clone ioctl (which exposes Btrfs' copy-on-write functionality). https://github.com/g2p/bedup
Probably, the package with it could include a script for cron to run deduplication regulalrly, say, every day (or week) at night -- which could be turned on by those who wish.
[slava@dubrhome ~]$ apt-cache search bedup i586-bedup - Deduplication for Btrfs bedup - Deduplication for Btrfs [slava@dubrhome ~]$ apt-cache show bedup Package: bedup Section: File tools Installed Size: 478992 Maintainer: Vitaly Lipatov <lav@altlinux.ru> Version: 0.9.0-alt1