You could also employ a different filesystem like ZFS or btrfs in tandem with the symlink-swapping strategy to achieve things like deduplication. Or, once you have deduplication at the filesystem level, just construct a new complete duplicate of the folder to represent the new version and use renaming to swap the old for the new, and poof -- atomic changes and versioning with de-duplication, all while continuing to be able to use standard filesystem paradigms and tools.