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Some users uses built-in remote terminal on Unix and Windows local hosts. On Unix user can select some text in terminal and paste via middle mouse button. On Windows it is more long action. I think we can emulate Unix-like copy&paste inside current terminal on Windows too.
Term _does_ honor middle-mouse click. It uses SwingUtilities.isMiddleMouseButton() to detect this. So perhaps on Windows SwingUtilities.isMiddleMouseButton() doesn't work? I've had similar reports, from Tim Boudreau, regarding the Mac.