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Looking to move from rsnapshot backups to something like backupninja. I'm having trouble finding a definitive answer on how to delete the rsnapshot backups.

From what I understand many of the files are hard links and not actual copies.

How can I delete /mnt/disk1/backups/* (daily.0, weekly.0, etc) without harming the original files?

Is it simply rm /mnt/disk1/backups/* -R?

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You are right about backup files being hard links and it is safe to just delete the backup directory.

Hard links are just pointers, so if a file have two hard links then the space occupied by this file will only be reclaimed by OS when both links are deleted.

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