You can run command line commands right from PhpStorm. Just configure the commands that fit your preferences and needs as a command line tool and register it in PhpStorm. You can have as many command line tools as you need.
Integration with command line tools is provided at the PhpStorm level, so once configured, a tool can be used in all your PhpStorm projects. Just activate or de-activate it when necessary depending on the needs of each specific project.
Integration with command line tools is supported via the Command Line Tool Support bundled plugin. The plugin is by default enabled. If not, enable it in the Plugin Configuration Wizard or the Plugins page of the Settings dialog box.