XDG Default Applications
xdg-mime
Print the .desktop filename of the application that is registered to open directories:
xdg-mime query default inode/directory
Associate directories with Nautilus (Files). This will modify ~/.config/mimetypes.list:
xdg-mime default org.gnome.Nautilus.desktop inode/directory
Example ~/.config/mimeapps.list
[Default Applications]
application/json=code.desktop
application/pdf=org.gnome.Evince.desktop
audio/mp3=music.desktop
audio/x-flac=music.desktop
image/jpeg=org.gnome.eog.desktop
image/png=org.gnome.eog.desktop
inode/directory=org.gnome.Nautilus.desktop
text/markdown=org.gnome.TextEditor.desktop
text/plain=org.gnome.TextEditor.desktop
video/mp4=io.github.vlc.desktop
video/ogg=io.github.vlc.desktop
video/quicktime=io.github.vlc.desktop
video/webm=io.github.vlc.desktop
video/x-m4v=io.github.vlc.desktop
video/x-matroska=io.github.vlc.desktop
If you want the change to be system-wide, run xdg-mime as root. This will modify /usr/share/applications/mimeapps.list.