location of Ubuntu OS code line that calls this message box to fore

That is not triggered by the OS but by the application doing the copying.
(The OS only provides a framebuffer devices, an array of pixels to fill).
On top of that runs the X server (providing primitives to graph stuff into the framebuffer).
On top of that runs the GUI Shell (Gnome, KDE, Motif etc.)  / Windows Manager
On top of that runs the GUI tools.

It depends on the app you are pasting into. That decides how it will handle the data.
That can be any app,  an Editor, a shell (command interpreter) window, IDE, LibreOffice, ....
If you paste some things to the Graphic shell then it may attempt to start some application for you. (Depending on the shell functionality).

X server can be replayed by something else (f.e. Wayland)
The GUI Shell can be changed if you don;t like Gnome take KDE, or any of the 20 or so shells there are.
Some are Lightweight (ie... provide less functionality, and are more handy to use on small system)

The GUI Shell may provide primitive actions & subroutines to ease the development of applications and provide a certain look & feel to all applications.
(Like File Open/ File Save dialogs, Message bx dialogs etc. etc.)

As Noci said, this is triggered by an Application, rather than the OS.

Since there's no context (what Application is generating the message), best suggestion will be this.

Check your Application's options to look for a force option, to force operations like file over writing.

Tip: My suggestion is likely a bad idea, because choosing a force option can obliterate files you don't mean to obliterate.

Use extreme caution with forced operations.

thank you for the responses........obviously i am just getting my feet wet for the first time but i CAN see that what you are saying is perfectly correct

beginning to look to me as if i need to pursue GNU core functionality and perhaps alter it.....  pretty deep and way beyond me at the moment but i'm chasing it