Is there a way to ensure that apps you close from the unity dock really close, by which I mean an "Ubuntu" setting rather than application specific ones. The two applications I notice this most with are Skype and Spotify, no matter how I close them they always linger, either in the top right corner or truly hidden where only a killall command will work.
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Just as a note, the reason that Skype and Spotify's icons don't disappear is because they're programmed with that in mind. They're expecting people to, in the case of Skype, want to leave it running so they get messages and notifications without needing to have a full window open, and, in the case of Spotify, they're expecting people will want to listen to music in the background without needing to having to have the full window open. – RPiAwesomeness Apr 21 '15 at 16:16
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I figured that is the case, but shouldn't there at least be the option to quit them? Minimising closes the window and leaves an icon present, quitting should quit. – Zack Newsham Apr 21 '15 at 16:23
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@ZackNewsham The app and process are separate. That's why it doesn't close. – TheWanderer Apr 21 '15 at 16:23
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@ZackNewsham I just answered showing how to fully quit them from the top bar icon menu thing. I'll look into making it possible to fully quit them from the dock. – RPiAwesomeness Apr 21 '15 at 16:24
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While I can't provide a solution to fully quit Skype & Spotify from the dock, I can show you how to fully quite them both.
Once you close the window, as you've seen, the program minimizes to the top bar. From there, you can quit them both.
Spotify:
Skype:
If you have no Skype icon, run this command:
sudo apt-get install sni-qt:i386
and then restart. It should enable the Skype icon.

RPiAwesomeness
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Thanks, I was aware of this for spotify, but my Skype does not appear there. – Zack Newsham Apr 21 '15 at 16:24
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@ZackNewsham Really? It just disappears? That's strange. How did you install Skype? – RPiAwesomeness Apr 21 '15 at 16:25
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I don't remember how it was installed. Perhaps I'll try an update. What is the official way to install Skype? – Zack Newsham Apr 21 '15 at 16:26
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@ZackNewsham Try running
sudo apt-get install sni-qt:i386
and restarting and see if you get the icon then. – RPiAwesomeness Apr 21 '15 at 16:27 -
@ZackNewsham If you do get the icon, could you comment and let me know? That would be great, I like to know if my answers have helped people or not :) – RPiAwesomeness Apr 21 '15 at 16:58
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It didn't initially but after a second restart I do see the icon up there. Thanks for your help – Zack Newsham Apr 21 '15 at 17:07
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@ZackNewsham No problem, glad I was able to help! If this answers your question, could you mark my answer as such? It makes it easier for future users to see if this worked or not, and it is the normal action if an answer resolves your issue. – RPiAwesomeness Apr 21 '15 at 22:22
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I will hold off on that for a while, as it doesnt really answer my question. As I still can't close apps from the dock, nor is there an identified unity setting that will allow this to be the case always (In fact I found an Ubuntu blog post that seemed to say they were explicitly moving away from the idea of "quitting"). I did upvote it though, as it was helpful. – Zack Newsham Apr 22 '15 at 15:52
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@ZackNewsham Fair enough. I'll keep looking into it, I remember something with editing the quicklists or something. – RPiAwesomeness Apr 22 '15 at 21:15