You can install this plugin into your CakePHP 3.x application using composer.
The recommended way to install composer packages is:
composer require skie/cakephp-phpstorm
After install plugin run
bin/cake CommandLine
to generate the custom xml file for PhpStorm Command Line Tools.
File stored into .idea/commandlinetools/Custom_ck.xml After that you should restart PhpStorm. After restart all shell comands should be available from command line tool (Ctrl+Shift+X) with detailed help.