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.
removing the .idea folder, and restarting the app did the trick for me
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.
I just experienced this problem in phpStorm 9 where I was trying to create a project from existing files but phpstorm could not see the directory. Very weird.
So what I did was I instead went to "create new project" and manually put in the location box the path to an existing directory. On the next screen it asked something like "directory exists, do you want to create project from these files?" and that worked.
Have you changed the scope dropdown value by any chance?
Here is how i did it in PHPStorm 2016.
Open the Settings / Preferences Dialog by pressing ⌘, or by choosing File | Settings for Windows and Linux or WebStorm | Preferences for OS X. Click the Directories node.
Then: