Same issue here with Ubuntu Gnome 15.10
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https://bugs.launchpad.net/bugs/1429153
Title:
Gedit won't stay in Favorites
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This is mostly likely a mismatch in defaults.list
** Also affects: gnome-shell (Ubuntu Vivid)
Importance: Undecided
Status: New
** No longer affects: gnome-shell (Ubuntu Vivid)
** Changed in: gnome-shell (Ubuntu Wily)
Status: New => Triaged
** Changed in: gnome-shell (Ubuntu
** Also affects: gnome-shell (Ubuntu)
Importance: Undecided
Status: New
** Also affects: gnome-shell (Ubuntu Wily)
Importance: Undecided
Status: New
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Bugs, which is subscribed to Ubuntu.