The same happens if I use a PHPstorm instead of gedit in the above
example. So it seems that other applications "take over" the  copy-paste
buffer and terminal is unable to write to it.

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https://bugs.launchpad.net/bugs/1723884

Title:
  Copy of text from terminal window does not copy

Status in gnome-terminal package in Ubuntu:
  New

Bug description:
  - do a default install of Ubuntu 17.10
  - open a terminal window
  - select some text, click and select "Copy"
  - go to any other application and try to paste the text

  Expected:
  The text is pasted

  Actual:
  There is no text pasted

  Problem happens with all text selection/copy methods that I can find,
  e.g. laptop touchpad, external wireless mouse, shift-ctrl-C. Using a
  brand new Dell Inspiron 14 5000 series laptop.

  Text can be copied fine from other application windows (e.g. gedit)
  and then pasted into the terminal window. So it seems to be just the
  copy operation in the terminal window that does not work.

  Also, I can't believe this is really broken and not reported, because
  many many people would quickly notice this. I can't think what I can
  do wrong to have caused this problem. But yet here I am?

  ProblemType: Bug
  DistroRelease: Ubuntu 17.10
  Package: gnome-terminal 3.24.2-0ubuntu4
  ProcVersionSignature: Ubuntu 4.13.0-15.16-generic 4.13.4
  Uname: Linux 4.13.0-15-generic x86_64
  ApportVersion: 2.20.7-0ubuntu3
  Architecture: amd64
  CurrentDesktop: ubuntu:GNOME
  Date: Mon Oct 16 14:10:48 2017
  ExecutablePath: /usr/lib/gnome-terminal/gnome-terminal-server
  InstallationDate: Installed on 2017-10-13 (2 days ago)
  InstallationMedia: Ubuntu 17.10 "Artful Aardvark" - Alpha amd64 (20170926)
  SourcePackage: gnome-terminal
  UpgradeStatus: No upgrade log present (probably fresh install)

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