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Hooooly shit. In Windows 7 you can't put a file called "abc.txt" in the folder if there is already a folder called "abc.txt".
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Yes, it would get pretty complex in some cases, especially when using command-line tools. While most commands are file or folder-specific, some might work for both and how would you tell the tool wether you want to target the file or folder? Sure, you can add a flag to the command but what if you forget it? GUI-based stuff would have less problems handling this situation but still, it would provide more headaches than convenience.
There's also backward compatibility problems with older systems when you do this, Windows still has 8-letter 'DOS' folders for similar reasons.
In theory it could be solved but it's better to avoid the confusion all together.
That's true, this is also why symlinking files and folders is so easy. All that does is create a pointer to another pointer somewhere on your hard drive.
From a very simple perspective, folders can contain content, it's just that their content is limited to other folders and files and that they can't do things like be executed for example.