There are 2 clipboard-like mechanisms in Linux - primary selection (copy by selecting text and paste by middle mouse button) and clipboard selection (copy by CTRL+C, paste by CTRL+V). Since I prefer using only the latter, I wanted to completely disable the primary selection.

Note: This solution (specifically the echo -n "" | xclip -i -selection primary part of it) clears the selection in GTK applications. This problem happens even when using the xsel tool instead of xclip. If you use this or a similar solution and see problems in selecting text in GTK applications, it may be related.

Install xclip and clipnotify, e.g. in Arch Linux:

pacman -S xclip clipnotify

Create the following script (e.g. in /home/user/clipboard_fix):

#!/bin/bash

set -e
set -u

while clipnotify; do
  echo -n "" | xclip -i -selection primary
  echo -n "" | xclip -i -selection secondary
done

The script:

• waits for the clipboard contents to change
• after each change, clears the contents of primary and secondary selections, while not touching the clipboard selection

Leave the script running in the background when X starts, e.g. add this to ~/.xinitrc:

/home/user/clipboard_fix &

For me, this mechanism avoids pasting some random content after I accidentally press the middle mouse button.

The clipboard selection (CTRL+C, CTRL+V) is actually supported in many applications, e.g.:

• GUI applications (Qt, GTK)
• terminology (terminal emulator)
• far2l (file manager) when running in --notty mode
• Visual Studio Code - in its terminal, it can be configured to CTRL+C and CTRL+V in File -> Preferences -> Keyboard Shortcuts

If some applications cannot work together correctly through the clipboard because of different data formats (targets), we can create a workaround by adding an automatic conversion to our script, e.g.:

CURRENT_TARGETS=$(xclip -o -t TARGETS -selection clipboard | tr '\n' '|')

if [ "${CURRENT_TARGETS}" == "text/plain;charset=utf-8|application/x-elementary-markup|" ]; then
  xclip -o -selection clipboard | xclip -i -selection clipboard -t STRING
fi