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I successfully changed several icons by adding .png files into the pixmaps folder, and editing the programs' Icon=.

Nautilus doesn't seem to follow that rule, and I am curious where does it pull its icons from, and how can I find out? It also has 3 nautilus Files files in usr/share/applications, and even more on the console list. Is it enough to just change the nautilus.desktop file, or will I have to change more?

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Nautilus is a GNOME file manager and using sudo allows for root access to otherwise locked folders due to permission error in Ubuntu.

In Ubuntu 16.04.2 LTS, the Nautilus icon is located here: /usr/share/icons/Humanity/apps/128/system-file-manager.svg

The smaller version of Nautilus icon is located in other folders, such as /apps/32/system-file-manager.svg

Another version of Nautilus icon (i.e. gastropod seashell) can be saved from here: https://upload.wikimedia.org/wikipedia/commons/thumb/3/32/Nautilus_icon.svg/120px-Nautilus_icon.svg.png

The Nautilus.desktop file looks like this:

[Desktop Entry]
Type=Application
Version=3.14.3
Name=GNOME Nautilus
GenericName=File Manager
Comment=Access Folders as Root
Icon=/usr/share/icons/Humanity/apps/128/system-file-manager.svg
Exec=gksudo nautilus /home
Terminal=false
Name[en_US]=Nautilus

Make sure to change Permissions tab, Owner: and Group: set to Read and Write, and check box for Execute: Allow executing file as program

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