I\'m using PhpStorm 6.0.3, and it doesn\'t show any directories in the Project Tool Window. They were there just a minute ago but I managed to make them disappear by clicking or
PHPStorm seems to do this in case of empty directories (at least if you actively delete a file inside of phpstorm).
As a temporary quick fix you can simply open the folder in explorer and create any empty file:
After you've done this, make sure you syncronize your project by right-clicking and selecting "Syncronize":
That should make your previously hidden folder visible and you can simply create your first actual file and just delete the empty file afterwards.