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debian disk is dying

The hardware needs to be returned to the factory for a warranty-covered replacement. I have an esata docking station and an esata hard drive I can put this system on though. I'm using the command line and figure I'll probably end up using cpio to do the backup. What maybe could be a problem with cpio are the /dev /proc /pts and another directory tree that needs all of its directories to copy over empty so when the system starts up for the first time on the usb interface it will create its own files inside those directory trees. I don't know how to get cpio to create those directories or directory trees but not copy existing files off the dying disk into those directories. I did download dar and could use it but would prefer to just have a complete mirrored backup I can run once the dying disk is removed. If it helps any, this is an AMD processor equipped machine. I read about the need for the directory trees being created empty in the dar tutorial.

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