Magento 2 – Code Formatting Settings for PHPStorm

Nothing specific to setup, in your server install xdebug debugger, make sure that you see it listed in phpinfo output in a file in your Magento root. Then turn on "Start listen for php debug connections" from Run menu or toolbar icon. Place your break points wherever you want. Use php storm bookmarklet to initiate debug session with cookie. If all is successful PhpStorm will popup on your break point whenever the code reaches it.

Namespace root is your most likely problem. PhpStorm absolutely supports the feature you're looking for, and it should work out of box.

Make sure your project encompasses the entire source code, then tell PhpStorm where to go looking, if it wasn't able to work it out on its own. See: https://www.jetbrains.com/help/phpstorm/2016.1/configuring-php-namespaces-in-a-project.html#d140255e161

Configuring Namespace Roots Manually

Open the Settings / Preferences Dialog by choosing File | Settings for Windows and Linux or PhpStorm | Preferences for OS X, and click Directories under Project:. The right-hand pane of the Directories page that opens shows all the content roots configured in the project. As a rule, there is one content root which is the root folder of the current project.

The central pane shows all the folders under the selected content root. Select the folder to be treated as the namespace root and click Sources.

It is perfectly fine to configure multiple source roots: PhpStorm will treat each of those as a namespace root and provide namespace hints for files underneath them. For example every subfolder of a vendor folder can be marked as a namespace root. In the example below, we have two namespace roots: one for the actual application and one for a vendor folder

At minimum, you want to set the 'vendor' folder as Sources, plus the app/code folder if it exists. Under normal circumstances, every module (and namespace) should be within those two locations.