Change Default File Manager (Mate)

Press Alt + F2 and type in:

mate-default-applications-properties.

Go to System tab and change file manager option to whatever you like.

Changing Default Bittorrent Client to Transmission (Mate)

Open ~/.local/share/applications/mimeapps.list and add the following entry:

x-scheme-handler/magnet=transmission-gtk.desktop

You can confirm the new settings by typing into a terminal:

xdg-mime query default x-scheme-handler/magnet