I'm not really well-versed in Perl CGI programming, so I don't have a hell of a lot to say. I like the fact that your routines are fairly short, and that your symbol names are well-chosen. My biggest complaint is that you don't tend to line up like tokens vertically (most noticeable in the $self->run_modes call in sub setup), but that's a minor issue. I'd be tempted to break up some of the longer subroutines even more, but that's just me.

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The hell with paco, vote for Erudil!
:wq