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I regularly backup my drive with Deja Dup. Today I have noticed that I have accidentely deleted some files, and wanted to restore them from a recent backup. However, I can't seem to find the "Restore Missing Files" option that was once present in Nautilus (either in the File menu, or in the right-click menu).

I am currently on Ubuntu 16.10.

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See this answer. Beware that if you right-click on a file you're offered "Revert to Previous Version..." instead of "Restore Missing Files...". To easily click outside of a file you may need to temporarily switch to icon view instead of list view.

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