Shell – Why is Terminal automatically executing the command after pasting text

For historical reasons, there are two selections¹, with different usage conventions:

• The PRIMARY selection automatically changes when you highlight some text with the mouse. There is no “copy” command, it's automatic.
• The CLIPBOARD selection changes only when you issue a “copy” command (keyboard shortcut or icon or menu entry).

Classic X11 applications such as urxvt support PRIMARY only. Modern X11 applications such as anything using Gtk/Gnome or Qt/KDE support CLIPBOARD and often, but not always, PRIMARY. The unfortunate consequence is that you can't directly copy-paste between CLIPBOARD-only applications and PRIMARY-only applications, and you can't easily copy-paste between CLIPBOARD-preferring applications and PRIMARY-only applications.

If you highlight text with the mouse in urxvt, you can paste it in Abiword with the middle mouse button (whereas the keyboard shortcut would paste the CLIPBOARD).

If you need to transfer text between selections, you have several methods:

• Use a GUI clipboard manager (Autocutsel, XFCE Clipmap, Gnome Glipper, KDE Klipper, Parcellite, …).
• Paste into an intermediate application that supports both and copy again.

• Use the command-line program xclip or xsel to copy the PRIMARY selection into the CLIPBOARD or vice versa.

  xclip -selection primary -o | xclip -selection clipboard -i
  xsel | xsel -b
  xclip -selection clipboard -o | xclip -selection primary -i
  xsel -b | xsel
  

¹ _{Even more, in fact, but only two that you'd encounter on a regular basis.}

This answer is not the most-specific for the user's question Please see my 2nd answer. I am leaving this here because it addresses the more general issue.

Per the comments to your original post, you need (1) a terminal emulator which supports bracketed paste and (2) corresponding support for whatever is running in the terminal, ie, vim, bash, zsh. Terminal emulators supporting bracketed paste (list to be updated based on comments to this post):

• xterm - since ??
• gnome-terminal - since ??
• putty - since 0.63 (2013-08-06 release date)

Applications supporting bracketed mode:

• vim
• zsh

For bash, StéphaneChazelas has put together a shell script to facilitate the detection of that mode and take appropriate action.

A more specific answer -- preventing lines from getting chopped off -- is unanswerable without knowing about the unix program that is running when you hit paste.

A clipboard manager maybe what you need.