@arspr, possibly some people are very anal about this kind of thing? Anyone who really wants their structure might also want the structure automatically enforced, if the right option is set.
The ability to set ebook-edit to enforce the Arrange in folders (a/k/a sorting) rules whenever files are opened/added would be a nice expansion of the current functionality,

but I agree most people will care just as little as they care about the ability to
manually sort.
Hey, just because Sigil did it doesn't make it wrong.

But choice is good.
Kovid, I just noticed that calibre_bookmarks.txt is being categorized as under "Text (HTML) files", which yanks it out of the META-INF folder. Kind of ironic that a calibre feature just attacked another calibre feature.
Anything which the File Browser sees as Miscellaneous should be ignored, I think. And only the stuff seen as Text should be getting moved by the Arrange feature.