Stephan Hochdörfer has a quick post to the bitExpert blog today showing you how to configure Xdebug+PHPStorm for CLI debugging, making it even easier to work with command-line PHP applications.
Current situation: I have no local webserver running and just php5-cli (plus a few extensions) installed as most of the development I do will make use of a Vagrant machine. From time to time I develop small tools or libs which I like to debug on the command line. This is an overview how I configured my Ubuntu 14.04 box to handle debugging with Xdebug and phpstorm.
He starts with helping you get Xdebug installed (via PECL) and configured for local debugging. Next he adds some variables to the .bashrc configuration file with the IDE and Xdebug configuration details. Finally he gives the instructions to get PHPStorm to play nicely with this setup via it's own "Servers" support.