If you are a user (like me) who runs both gnome and kde together and finds that some of the auto starting applications meant for either gnome only or kde only are running in both desktops , then /etc/xdg/autostart is the directory to look for.
In this directory we can see .desktop files of auto starting applications. For preventing an application from auto starting in KDE edit the applications .desktop file and add OnlyShowIn=GNOME;
For preventing a KDE application from running in Gnome add
OnlyShowIn=KDE; to that applications .desktop file and you are done
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