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I've tried using Recuva, Undelete Plus, and some other tools. But it seems these tools are unable to find the content stored in .hg or .git folder, I can only recover .hgignore or .gitignore files. Does this have anything to do with NTFS? Is there any way to recover these files? Please advise, thanks.

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Usually you can only recover files, not folders, due to the differences in how they are stored. For git, search for files with filenames like 97e976b99de7a2e22e83ba619a019571ce913a or pack-75910f9afc31862111442119c47ca55b9ec9769d.pack, those contain the actual data. –  grawity Jun 28 '11 at 9:33

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