Is there a way to save my workspaces(the windows I have open) so that when I restart my computer, all my of the windows will be reopened and positioned in the same way?
I have ubuntu 11.04 and run GNOME
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You can save which applications are opened when you shut down, by activating this option:
Automatically remember running applications when logging out in System -> Preferences -> Startup Applications -> Options
Nevertheless, this won't remember which workspace each application was running. To do that you can use the compiz plugin "Place Window" to configure "Windows with fixed viewport" based on the application name.
install ccsm and plugins:
sudo apt-get install compizconfig-settings-manager python-compizconfig compiz-fusion-plugins-extra compiz-fusion-bcop compiz-fusion-plugins-main compizconfig-backend-gconf
You must create a rule for each application, which will then open in the specified viewport (workspace) whenever you start it.