I'm having one issue on Mac OS X El Capitan with Eclipse Mars and menu windows. When a menu window opens a new window, it shows in the back of the first one, and moves along with it (if I move the first one, the second one moves with it, but not the other way around). So there are two possible scenarios. If the second window shows a bit (like in this image), you still can move it and then interact with it, but if the second window is totally hidden (like this one when clicking 'Advanced'), then there's nothing you can do, since it seems impossible to put it on top. Is this a known bug or is there a solution for it?
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1PS Please follow http://meta.stackexchange.com/questions/75491/how-to-upload-an-image-to-a-post for how to put images in a post. In particular SO has a pro account with imgur so that images never disappear. – Jonah Graham Nov 09 '15 at 13:47