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The author of this question states in a comment that he solved the problem of adding an app to startup by linking its desktop file to ~/.config/autostart.

Trying to test that I see on my system a big difference between what's there and what really is auto-starting on my system, as some of the apps there are not in the startup list at all, some are disabled, and one app is auto-starting (pcmanfm daemon) without being there.

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What does this mean? Is ~/.config/autostart obsolete?

When I delete all desktop files there, the startup list is also emptied.

How does it work?

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There are different places from where stuff is autostarted. There are /etc/xdg/autostart and ~/.config/autostart that I know of.

All the stuff, that's not shown in the Startup list is in /etc/xdg/autostart probably. And the apps that are in the settings list are probably in ~/.config/autostart

~/.config/autostart is for applications that only start on login of the current user, while the ones from etc/xdg/autostart are started for every one.

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