Disk Usage Analyzer stealing mimetype assocation inode/directory from Nautilus
To me it seems the appropriate way is to define Nautilus as the default application to handle the mimetype inode/directory. This can be done via console with
xdg-mime default nautilus.desktop inode/directory
What it does is adding the following line to .local/share/applications/mimeapps.list
inode/directory=nautilus.desktop
About accepted answer: I don't know what adding a colon and a number to the mimetype in the baobab desktop file does, but if it's just disabling the unwanted behaviour this won't be sufficient. I can imagine another application hijacking/overriding the mimetype assocation again.
Another point is that you have all your defaults defined in one place.
edit /usr/share/applications/baobab.desktop
and change
MimeType=inode/directory;
with
MimeType=inode/directory:1;
then run this command:
sudo update-desktop-database -q