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Linux systems provide several different buffers where programs save the clipboard information. It is sometimes confusing, how the clipboard interacts between different programs.

While you can copy and paste from Firefox to Emacs with the middle mouse button, it is necessary to press Ctrl+C and Ctrl+Y to copy and paste from Adobe Acrobat Reader to Emacs.

It would be nice to have one clipboard buffer, how can this be configured?

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linux (the kernel) does not have any clipboard buffers. what you are probably getting confused with is the X11 selection buffers, there are three of them: primary, secondary, and clipboard. If you just want this to go away look at http://www.nongnu.org/autocutsel/ which synchronizes the primary with the clipboard. but as far as the different keystrokes between applications, you have to put up with the differences.

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