One thing that occurs to me is that if the MIME body contains HTML, you could strip the plain text message out completely, alter the HTML as you need it, and then insert a new plain text message derived from your altered HTML. I suggest this as an alternative to stripping the HTML because the more simple formats can be derived from the more complex ones with relatively little extra effort (it doesn't work in the other direction). I guess I'd suggest HTML::TokeParser or HTML::TokeParser::Simple for that job.

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Allolex