The term directory is hardly ever used anymore and both Windows and OSX use the term folder. Although they can be used interchangeably since they mean the same thing to a user, they technically are not the same. See also: http://superuser.com/questions/169457/directory-vs-folder
Both are a metaphor. While on a filesystem level the term directory (a listing of information) makes a lot of sense, in a GUI the idea of a "folding cover or holder" is a closer match to its use and graphical representation.
In cases such as these it's important to look at the environment your application will be used. Usually a user will spend more time in the OS and all other applications taken together than in your specific application. If the OS always talks about folders, you shouldn't be talking about directories.
You should use either one or the other. In general a "thing" or concept in an application should always have the same name throughout your application. Eg. in social media the terms "message" and "post" could be seen as synonyms, users may call the post a message or the other way around, but the application itself should be clear about wether it's the one or the other.