Роман

Правой клавишей по папке в которой хотите создать класс - New - PHP class.

Как вариант добавить в Exec=sh -c "/opt/PhpStorm-141.2462/bin/phpstorm.sh /var/www/Project3/"

[Desktop Entry]
Version=1.0
Type=Application
Name=PhpStorm
Icon=/opt/PhpStorm-141.2462/bin/webide.png
Exec="/opt/PhpStorm-141.2462/bin/phpstorm.sh"
Comment=Develop with pleasure!!!
Categories=Development;IDE;
Terminal=false
StartupWMClass=jetbrains-phpstorm

Actions=Project1;Project2;Project3;

[Desktop Action Project1]
Name=Project1
Exec=sh -c "/opt/PhpStorm-141.2462/bin/phpstorm.sh /var/www/Project1/"
OnlyShowIn=Unity;

[Desktop Action Project2]
Name=Project2
Exec=sh -c "/opt/PhpStorm-141.2462/bin/phpstorm.sh /var/www/Project2/"
OnlyShowIn=Unity;

[Desktop Action Project3]
Name=Project3
Exec=sh -c "/opt/PhpStorm-141.2462/bin/phpstorm.sh /var/www/Project3/"
OnlyShowIn=Unity;