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
Go to PhpStorm setting(Ctrl+Alt+s)
type and select 'file types' not 'other file types'!(Editor > File Types)
in 'Ignore files and folders' remove all extension you need(i remove all!).
Apply it and you can see all your files in PhpStorm