I wonder the situation can be fixed: I have Ubuntu 21.04 with Kicad Nightly. The OS considers .kicad_pro files as plain text and tries to open those with any default text editor (Atom / Sublime / Vim, etc.).
If I Right-Click on the project file and than: -> “Properties” -> “Open With” -> “KiCad nightly” -> “Set as default” that systems tries to open each text file with KiCad. Any suggestions with this?
What’s probably happening is that .kicad_pro is mapped to the mime type text/plain and various applications like text editors have been registered to handle this mime type. When you edited the rule you were editing for all objects of mime type text/plain.
What has to happen is that .kicad_pro has to map to a different mime type, I think applicaion/kicad, and kicad has to be registered to handle files of this mime type. As to how this is done, I’ve never looked into it since I use the KiCad interface or the command line interface, rather than the “object oriented” desktop interface. Sorry I can’t help further.