thanks a lot Andreas,

I've now been trying .../startup/windows.js , which handles the 
tm-open-window message
couldn't I also try to register it from within there, when the window gets 
opened?

I'll take a look at your tips, the second seems more appropriate to me, 
changing that much like in (1) is a bit out of my skill-scope and I guess 
it would need to change many other things, too

Hi Simon,
>
> that is almost the right place yes, if you have a look at 
> core/modules/startup/startup.js [1], you will see that it initializes it 
> without the rootElement being given anyway. The next problem is that all 
> widgets regardless of the window they are rendered in will use 
> $tw.popup.triggerPopup(), so we can't have multiple popup handler (i.e. 
> one per window). The actual event listener however will be registered in 
> $tw.popup.show().
>
> As it stands I see two ways you could make the core properly handle this:
>
>    - Turn the global window variable in core/modules/startup/window.js 
>    into $tw.openWindows and make sure that all open windows including the 
>    main one are listed there and then have the Popup mechanism iterate 
> through 
>    these and register itself (to all of them). 
>    - Have the Popup mechanism use [2] to register itself to the 
>    appropriate window by default and only change this if the rootElement 
>    option was set. (Not sure how well this would work in other browsers, but 
>    it would require the least change) 
>
> [1] 
> https://github.com/Jermolene/TiddlyWiki5/blob/master/core/modules/startup/startup.js#L118
>
> [2] https://developer.mozilla.org/en-US/docs/Web/API/Node/ownerDocument
>

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