You would have felt a number of times that different PHP projects have different priorities. You got it right. A website development project, for example, would require a running web server configuration, and it might not require command-line PHP.
A simple PHP project, on the other hand, would require command-line PHP, without a web server, and the list of directories could be limited to some folders in a hierarchy. The point here is that there are different projects with different dependencies and settings. Having a working set makes PhpStorm behave appropriately for the project currently open.
If you monitor the Settings pane closely, you will notice that there are two major sections. One is the project-settings section, where you make settings according to your project. This helps a great deal. PhpStorm builds an index for every project. If you create a proper working set for your project, you will help PhpStorm to build a more precise...