1) When doing a pkg upgrade in order to get an up-to-date system, a lot of gnome depends are added : nautilus, brasero, cheese, shotwell.
2) A Gnome session is added ?!
3) Nautilus is conflicting with Caja about desktop shortcuts. I have to remove nautilus, brasero and others gnome only depends to fix this.
4) LibreOffice is switched to "high constrast" theme. Removing its configuration files doesn't fix this bug.
5) Sometimes, there is a lot of Caja windows opening on start. Known bug of Caja 1.6.x if I remember well.