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I deleted and later re-created the Documents folder in my home directory. It no longer appears in the Files quicklist. You can see in the screen shot below that several bookmarks are present among the home directories, but Documents is not there anymore. I can add and remove bookmarks in Nautilus and they appear and disappear from the quicklist, which is the expected behaviour.

How do I restore the original functionality such that existing default user directories (Desktop, Documents, Music, etc...) are listed in the Files quicklist along with dynamically added Nautilus bookmarks?

files-quicklist

I know I can create a custom quicklist for Files by manually creating and editing a .desktop file ~/.local/share/applications/nautilus, but this gives me a static quicklist (which may not pick up newly added Nautilus bookmarks?).

A note about the default user directories - once deleted, re-creating them is not the same as if the originals were left in place. The new folder icons are generic (easily fixed) and an edit has to be made to ~/.config/user-dirs.dirs to restore them to Nautilus' Places menu, but I cannot figure out how to get them back in the Files quicklist.

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Reset to default
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After some trial and error I've learned that the default user directories are not re-created in ~/.config/gtk-3.0/bookmarks like new Nautilus bookmarks are, and manually re-adding them to this file fixes this issue with the Files quicklist.

Follow the format of the existing folders, so for example I opened the bookmarks with nano ~/.config/gtk-3.0/bookmarks and put the line file:///home/tom/Documents at the top of the file and this fixed it (change the username in the example to yours, obviously). The change persists across reboots and new bookmarks continue to work as expected.

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