Remove folders from left panel in Nautilus

This list gets created by analyzing .desktop files located at:

/usr/share/applications
~/.local/share/applications

There might be more than one usecase per application, take for example the media player banshee which has three .desktop files by default:

$ ls -1 /usr/share/applications/banshee*
/usr/share/applications/banshee-1-audiocd.desktop
/usr/share/applications/banshee-1.desktop
/usr/share/applications/banshee-1-media-player.desktop

The only difference between those files is the starting parameter and the MimeType list.

• banshee-1.desktop: General media files
• banshee-1-audiocd.desktop: Audio CD's
• banshee-1-media-player.desktop Audio player (Also used by rhythmbox, vlc, and others)

So we have three 'Banshee Media Player' in the 'Open with' list (and maybe also in the 'Main Menu').

The other way of filling this space is by creating personal .desktop files in ~/.local/share/applications. Either manually or by using a tool. alacarte (or right-click on 'Main Menu' -> 'Edit Menu') is one of those.

Every time you create or move an application within alacarte, a new .desktop file gets placed inside ~/.local/share/applications. Disabling an application will "remove" it from the 'Main Menu', but not from the 'Open with' list.
But the 'Delete' button does, by creating a identical copy from /usr/share/applications into ~/.local/share/applications and adding Hidden=true to the .desktop file, thus "overwriting" the system-wide inherited values.

Deleting two of those entries from alacarte results in:

$ ls -1 ~/.local/share/applications/banshee*
/home/user/.local/share/applications/banshee-1-audiocd.desktop
/home/user/.local/share/applications/banshee-1-media-player.desktop

Removing any entries from ~/.local/share/applications will reverse to the preexisting state (three banshee items).

If you really don't have any duplicates in those two folders, try removing any duplicates from alacarte or playing with the Hidden=true option in the corresponding .desktop files.

eOS should support xdg-mime command which you can use to change the default file manager. Try these commands:

# what's the current default file manager?
xdg-mime query default inode/directory

# set nautilus as a default file manager
xdg-mime default nautilus.desktop inode/directory application/x-gnome-saved-search