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the tag system-tray refers to the upper panel, and the panel refers to the upper panel.

So why do they both exist?

like this question: it has system-tray listed and not upper panel?!

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    System tray shouldn't be a tag in the first place. Notification area (deprecated, but still applies for 10.04, 10.10) and Indicator applets. – Thomas Boxley Jan 2 '12 at 11:20
  • Perhaps some tag synonyms should be suggested? – Christopher Kyle Horton Jan 2 '12 at 12:24
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    I've untagged everything with system-tray and tray. – Jorge Castro Jan 2 '12 at 20:42
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The panel is the entire grey bar that spans the top of your screen. The "system-tray" is only the indicator area, where you have icons and stuff. In Unity, it isn't so easy to spot the difference, but in Gnome Panel, for instance, this area is a panel applet that can be moved around. The same is true for Xfce and LXDE, so in those environments, the difference is more noticeable.

  • the indicator area and the grey area are the same for me... – Alvar Jan 2 '12 at 15:02
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    Disagreeing with Alvar, they do look the same in Unity like Jo-Erlend indicated, but they differ exactly in how they say. The top right section that holds the icons such as the sound, network, mail, battery, etc. is not the same as the remainder of the gray area to the left of it, which is the panel. The panel contains the system-tray. Subtle difference. – Beanow Jan 3 '12 at 22:55

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