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
My USB flash drive decided to randomly disconnect itself while I was opening up the project, then I plugged it back in and no directories were showing up. Just the default files like all the .git files, .htaccess, and the index.php.
By going to File > Settings > Project: ProjectName > Directories. There was no longer any content root. I just had to click "Add Content Root" select my root folder and I was able to see everything again :)
Also it seems people have excluded directories like their content root or individual files which can be managed through the same settings.