A file cannot (in general) contain other files or folders in the traditional sense. A zip or other archive file can contain other files or folders and a document file can have a file in it as an embedded object, but these are special applications.

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There is no specific collective noun for folders, in which case a noun suitable for the situation is used, for example a drawer of folders, a pack of folders, a box of folders, etc.

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There are many types of pocket folders available. There are 2-pocket, tri-pocket, folders with holes and without, colored folders, and folders with pictures on the cover.