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Why do applications like synaptic (and other that need root privilege) have their menus in the window instead of top panel? Is it going to change or will it stay like that to indicate that user is on root privileges?

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For an application to use the global menu the environment variable $UBUNTU_MENUPROXY needs to be set to to the name of the menuproxy library to be used. For security reasons this variable is cleared when using sudo etc. to run a program as root.

As a side effect this indicates which programs are run as root, otherwise it may be not always clear that the items in the global menu belong to a program running as root.

As this are good reasons for the current behaviour I don't expect it to be changed.

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There's also a bug report about this on Launchpad. –  htorque May 5 '11 at 21:16
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