Is there a way to set up a keyboard shortcut for closing the file?
File > Close does not close the file but the tab, so does Cmd+W.
A Python solution perhaps?
Glyphs.documents[0].close()
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The keyboard command cmd+W should only close the current tab. This is the same as it always was and as it is in Safari.
If you need to close the window without closing all tabs first, use the close button on the window.