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I'm running into issues where if I have two applications running, where one is smaller and in the foreground, and I click on the window in the background, it does not move into the foreground. For example, if I have a terminal window on top of Firefox, and I click on the webpage in the background, Firefox gains focus but the terminal is still visible on top of Firefox. Is there a way to change this setting so that clicked on applications are always on top?

Note: If I click on the title bar, the application does in fact move to the top (in front of the terminal for instance).

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As of 14.04, clicking the title bar no longer brings the window to front if this option is enabled. I really feel like the Ubuntu team needs some sloppy-focus people on it so that these things can get caught earlier. –  rich remer 15 hours ago
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2 Answers

I believe the options for what I want to happen are selected, but for some reason unity doesn't use them properly (this may have something to do with upgrading from 12.04 instead of using a clean install). I had this problem with alt+click after upgrading, even though I changed the setting so it worked on 12.04. I went into the dconf editor, twiddled some settings but ultimately didn't change them, and now clicking on a window works as expected.

sudo apt-get install dconf-editor

Now run dconf Editor, and navigate to the relevant settings:

org->gnome->desktop->wm->preferences

Now change "focus mode" and "raise-on-click" to something and then set them back to default.

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Maybe you've that application fixed in the top layer. I do not exactly know how to put back in the same layer as the other applications because I'm using LXDE and not Gnome. But I guess in Gnome it can be done the same way. You can achieve the menu by right clicking on the title bar.

enter image description here

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No, the application on top (say a terminal) is not set to always on top. I can put something else in the foreground with alt-tab or by clicking the title bar. –  Brad Oct 21 '12 at 19:39
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