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I've accidentally removed all my home directory (don't judge!). My early search results led me to applications like extundelete and photorec. But the results were not acceptable. extundelete exits unexpectedly (without doing anything) and photorec recovers files in a flat structure. I wonder if there's an application which recovers files and folders together. My lost archive is consisted of thousands of files which are worthless if they are not structured in the original folders!

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Did you try testdisk. I have used Testdisk beofore to recover folder structures. http://www.bootmed.com/bootmed/tutorials-11/how-to-recover-deleted-files-with-testdisk/

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    According to this and this wiki pages, it works only with FAT, exFAT, NTFS and ext2 filesystems. – Giorgi Gzirishvili Mar 5 '15 at 15:29
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As you accidentally deleted the contents of home directory, you should be using extundelete from another OS or a live-CD/live-USB. Using extundelete from within the same OS where the partition is mounted, can make it behave wierdly.

I am posting this as an answer only because the question says that the extundelete exists unexpectedly without saying anything.

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