Emacs fails to respond, because it is buzy truncating a very large
    undo list. My emacs doesnt respond to c-g during this operation, and
    maybe that is normal behaviour.

It is strange that the undo list could get so big
that traversing it takes such a long time
without having been truncated previously.

Could you investigate how that happens?  For instance, could you use
GDB to call Flength on the Lisp_Object value of the undo list itself?
What is the value?

    My uninformed view of the problem is that undo information shouldnt be
    kept for process output, only for user modifications to the buffer.

I tend to agree.

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