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On my system (Ubuntu 14.04.1 LTS), the file you want is found at ~/.config/gtk-3.0/bookmarks Older versions used to keep this in ~/.gtk-bookmarks. Entries are URIs, so filepaths must be absolute and prefixed with file://.
Just drag and drop the files to the bottom left when at a folder! (Nautilus 2.32.0) I also posted the screenshots at gonorthwork/view for future archive reference:
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