File formats in Finder

While trying to open a file in Xcode (because no application could be found on double-click), my Finder stopped responding. After a forced restart, many files are now presented like folders. Good example perhaps : HD/System/Library/Frameworks/ : all .frameworks files that used to acquire a Ctrl-Click to Show Contents, are now accessible as regular folders and show their contents straight away.
So far, I did the basic steps like restart, zap the PRAM, trashed the Finder prefs. My system runs smoothly, no problem. It's just a bit strange (even scary) to see these "protected" folders pop up like they do right now.
Does anyone know what went wrong, and how I'd go about to fix things ?
TIA

Thank you, Mitch.
The file I was trying to open was a VectorWorks plugin, with the extension .vwplugin - it's icon used to look like a Lego cube.
While other VectorWorks plugins (.vsm and .vso) can be opened in TextEdit, this one couldn't - so I dragged it over Xcode, to no aveal.

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