I'm not sure exactly how much this helps you, but
Mail::Audit takes its input on STDIN, and the
two usual ways for remote clients to talk to mail servers,
IMAP and
POP3, are represented in CPAN.
It shouldn't be difficult to write a Perl script to grab
your mail and run it through whatever you please... the
difficulty, to my mind, would be getting your mailreader
to play nicely with Mail::Audit, which AFAIK only
writes to various Unixy formats of mailbox.
Update: You should be able to download a copy of
each message via IMAP, filter it through Mail::Audit
and/or friends, and based on the results keep it, move it
around, or delete it, also via IMAP (or more specifically,
via Mail::IMAPClient).
--
The hell with paco, vote for Erudil!
:wq