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When I first found out about the "hard link" option for recent releases of rsync, I got very excited, and soon discovered Dirvish, which was good enough.
The other option I found requires a custom-patched rsync client. (ugh) While this does enhance security, it certainly doesn't make it easy, which is the primary goal of this project.
Since writing BackupBuddy, and getting feedback from users and potential users, I've come across a number of other backup options. The first I'll discuss is rdiff-backup.
Rdiff-backup uses python instead of PHP. Otherwise, it's very similar to backup-buddy. I don't know how easy or configurable it is, compared to BackupBuddy.
BackupPC is the project I was looking for when I wrote Backup Buddy. If I didn't already write, setup, and start using BackupBuddy, I would have used BackupPC, and this is the only project I'd consider switching to from Backup Buddy.