I have been starting to explore how http://drupalconsole.com/ can be better integrated with the Command Line Tool, my progess is being recorded over at https://github.com/hechoendrupal/DrupalConsole/issues/1079.
Drupal Console uses the Symfony Console and as shown in the screenshots, see the github issue, its global commands are picked up automatically. However, the goal is to also be able to use the code generation and other project specific features it also offers.
I would be greatful for pointers to where I can find documentation about how to give Drupal Console the project path so it can recognize the drupal site project so code generation and other goodies also will be available from the PhpStorm Command Line Tool as is when using Drush.
If there are any tutorials about how to develope Command Line Tool integration I would be very happy for pointers to that too.