I totally agree with your example # 2.A file is one specific thing, and a folder is what you would keep the files in.
Example 1: A file may be a piece of paper, and a folder would be what you keep several of these files in. The exception is: If all the files in the folder are regarding the same thing, you might use the term "file" to refer to the entire folder.
Example 2: In computers, a file is one particular document or picture or spreadsheet or unit, and a folder contains many of these files.
I think this is what I was trying to say, but you've explained it a lot betterI totally agree with your example # 2.
However, regarding example # 1, perhaps our terminology in AE is different from BE. In the U.S., a piece of paper is a "document", documents relating to each other in a similar way make up a "file". The documents in a file might be physically stored together in a "folder", or "file folder".