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I opened System ➜ Preferences ➜ Startup Applications ➜ Options and clicked on Remember Currently Running Application. I suppose this makes Ubuntu memorize (save a list on some place in disk) all currently running applications and when you reboot your computer, the OS starts with everything in that list.

Now I want to get rid of it. Of course I can close all applications which I do not want to start in startup, and click Remember currently running Applications again, but this doesn't seem to work as expected. For example, Yakuake opens differently if I do that.

What I want is to completely turn off session saving. Maybe I can delete the stored information somehow?

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From man gnome-session:

The gnome-session program starts up the GNOME desktop environment. This command is typically executed by your login manager (either gdm, xdm, or from your X startup scripts). It will load either your saved session, or it will provide a default session for the user as defined by the system administrator (or the default GNOME installation on your system).

The default session is defined in the GConf keys under /desktop/gnome/session. When saving a session, gnome-session saves the currently running applications in the $XDG_CONFIG_HOME/gnome-session/saved-session directory.

gnome-session is an X11R6 session manager. It can manage GNOME applications as well as any X11R6 SM compliant.

(Emphasis mine)

By default $XDG_CONFIG_HOME is ~/.config so that is where the saved applications data is stored.

Remove all the files in that folder to "forget" the last running applications:

rm ~/.config/gnome-session/saved-session/*
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