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
I just solved a similar problem with Webstorm (Windows version 10.0.1) in a Cordova project. I created a new directory within the www folder, did not add any files and closed Webstorm. When I restarted Webstorm the next day, the new folder was invisible but existed as Webstorm refused to create a new one with an " ... already exists" error message and the file was listed as visible in the directories settings.
I solved the problem this way: Closed Webstorm -> Added a file to the empty folder with the Windows file browser -> Opened Web Storm -> The folder and the file was shown.