I'm using phpstorm 7.1.3
As far as I know project can have at least 2 directories - one with project settings file (the .idea folder) and the one you can set in Project settings -> Directories. I have such situation (those 2 folders are different) and when I go for example into Project settings -> Compass support there is "..." to opn select file dialog. But it seems it's impossible to select file in that way because path is set to directory with .idea folder and I cannot go anyway to directory with project content. Even if I click "Project directory icon" it won't change anything. The only solutions is not to use "..." and to paste file with path manually
On the other hand in File watchers when I want to set "Working directory" I can select any path I want but again when I click "Project directory icon" it goes to directory with .idea file.
I think the solution will be in that situation that clicking on "Project directory icon" would change directories (for example 1st click go to folder with .idea file, 2nd click go to 1st content root, 3rg click go to 2nd content root(if any), ... x click go to beginning - to folder with .idea file)