You can make NEMO as default file manager in this way (when you have Linux Mint 13 installed and you have both Nemo & Nautilus):
1.) You can run this command in Terminal to show the default app for folder:
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xdg-mime query default inode/directory
By default, the output of the command in Linux Mint 13 should be
nautilus.desktop.
2.) When you have Nemo installed on your system and want to set Nemo as the default file manager, run this command in Terminal:
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xdg-mime default nemo.desktop inode/directory application/x-gnome-saved-search
3.) Now, you can check if NEMO is default file manager:
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xdg-mime query default inode/directory
Now it writes that NEMO is default file manager
4.) To test the result, run this command:
That command should launch Nemo showing your home directory.
5.) If you want to stop Nautilus from handling the desktop and want to set Nemo instead, you can do the following (in Linux Mint 13, Nautilus is set to handle desktop by default (to manage desktop icons, menu, etc), and if you have Nemo installed, there will be a conflict, both will be automatically loaded every time you logging in, to take control of the desktop):
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gsettings set org.gnome.desktop.background show-desktop-icons false
6.) Make sure Nemo is set to handle desktop:
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gsettings set org.nemo.desktop show-desktop-icons true
That's it!
P.S. If you want that NEMO work when you press icon on panel just replace application name from
nautilus %U to
nemo %U.