Oh, this problem bothers me for a long time too:
I'm using ob-axiom from axiom-environment in Org-mode,
the numbering causes unwanted changes that pollutes my
git history.
By using
)boot $IOindex := nil
)set message prompt plain
in Org-mode, following changes are needed for axiom-environment:
(setq axiom-process-prompt-regexp "^.*(\\([[:digit:]]+\\|NIL\\)) ->\\|^->")
BTW, I'm not sure if the ".*" can be removed.
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