Comment 1 for bug 397724

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Przemek K. (azrael) wrote : Re: clipboard uses both selection and traditional clipboard

The mouse-selection clipboard is not specific to terminal. It works in many more applications - ie. Firefox.
It's not a compatibility layer. It's a consensus which was reached by developers.
http://freedesktop.org/wiki/Specifications/clipboards-spec?action=show
And it's not specific to Gnome - it's a part of Xorg.
I agree that having 2 clipboards might be misleading to users.
But ctrl-c and other shortcuts won't go away from the terminal. There is no chance for that. As far as I remember, this is a basic functionality defined in the POSIX standard.
People who use the terminal emulator are usually expert users and they will expect ctrl-c (and others) to work as in normal Unix/Linux terminal (not X).
Also, these expert users will know how X clipboards work. And they won't like using 2 clicks to achieve something that previously worked with just 1 click.
Ordinary Ubuntu users will not be required to run the terminal.