Problems with using xdg-mime default. The default was successfully set but it is not used via xdg-open

In my case the change wouldn't work:

$ xdg-mime default evince.desktop application/pdf

Running with debugging on will show you the files queried:

$ XDG_UTILS_DEBUG_LEVEL=2 xdg-mime query default application/pdf
Checking /usr/local/share//applications/defaults.list and /usr/local/share//applications/mimeinfo.cache
Checking /usr/local/share//applications/defaults.list and /usr/local/share//applications/mimeinfo.cache
Checking /usr/share//applications/defaults.list and /usr/share//applications/mimeinfo.cache
libreoffice-draw.desktop

Looking in that last file (where the match was found) gave me a hint:

$ grep application/pdf /usr/share/applications/mimeinfo.cache
application/pdf=libreoffice-draw.desktop;gimp.desktop;org.gnome.Evince.desktop;inkscape.desktop;

It's not called evince.desktop anymore, now it's org.gnome.Evince.desktop!

Once again, now using the new name:

$ xdg-mime default org.gnome.Evince.desktop application/pdf

$ XDG_UTILS_DEBUG_LEVEL=2 xdg-mime query default application/pdf
Checking ~/.config/mimeapps.list
org.gnome.Evince.desktop

Much better!

For me, further to running xdg-mime default caja.desktop inode/directory, it was running

update-desktop-database ~/.local/share/applications/

which finally updated the default application.

After this, running xdg-mime query default inode/directory now showed the new default application.