Thanks for the research, that looks like the cause of the Gnome problem and why it works just fine on other compositors that don't try to enforce their idea of how things should work.

Should a new issue be filed specifically to request the XDG Activation protocol be supported in Geany?

It should not need anything in Geany. GTK is what is communicating with the Wayland compositor (or X11 or Windows or Macos) but Geany does not know which backend is being used by GTK, and also there is no way of passing a token to GTK when requesting focus.

GTK knows which backend it is using and if it should get the token and supply it to the compositor on Wayland or not on other platforms. Probably GTK hasn't caught up with the activation yet, and the Wayland activation protocol is still "Warning! The protocol described in this file is currently in the testing phase.". And if/when it is added it will be to GTK4, GTK3 which is used by Geany will probably never get the capability.

So its probably not worth adding a Geany issue that will likely bitrot, but maybe you could raise it with GTK.

PS I'm not sure it will work anyway, how does Nautilus know which process will want to focus, its the first Geany that subsequent files open in new tabs, not the no GUI process that Nautilus runs that sends the request to the first Geany. So how does Nautilus know what window to get the token for?

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