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I was mostly referring to the fact that filesystem kind of enforces hierarchy, so you have it even if you dislike it. When I'm sorting out the mess that is my hard drive I defenitely value information about hierarchy overlap (due to (incomplete) copies), but I still have not found a tool that would help me an I can't imagine a query language that would be helpful.

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I'm not sure about a file system enforcing hierarchy. Historically, they didn't even support directories at first.

Which use cases would a query language fail to help with?

Hierarchy is the only tool it gives, you can't really have one dir with all your files, unless there's very few of them.

My typical scenario is multiple copies of something in progress, like traveling with friends, copying photos to each other phones on the way and then downloading the whole mess to one computer. Query language would give me precise information for every file but it's overwhelming.

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