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Is there a way to get gnome shell components (panel, message tray) to be appear below the popup menus of other applications such as Java and Gtk Apps.

The problem is when there are gtk apps which have tray icons. The popup menu tends to appear below the message tray. This was ok in 3.6 because the message tray hides as soon as the icon is clicked. But the top bar is still a problem for large menus.

When running eclipse with lot of options in the context menu, the top most items including the scroll button are under the top bar.

Is there any thing I can change in the main.js or panel.js to get things below the popup menus?

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I have manage to solve this issue by merging some fixes from the cinnaman desktop to gnome-shell. How they have solved it was by introducing a new window group which will act as the parent to the gnome shell stage and the popup menus are shown in that top most window group. This will make the popup menu appear on top of gnome shell panel. The changes are in gnome-shell project and the mutter project.

I have documented the steps for solving it in one of my blog posts

http://gaps-blog.blogspot.com/2012/12/gnome-shell-popup-menu-problem-solved.html

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Whilst this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference. –  slhck Jan 6 '13 at 14:06

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