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my $path = "./mail";
my $bkup = "./backup";
...
    rename "$path/$mbox", "$bkup/$mbox";
    system( "perl -ne 'print if /^From/..-1' $bkup/$mbox > $path/$mbox
+" );
}

for my $mbox ( grep { -f "$path/$_" and -s _ } readdir MAILDIR )
{
...
    rename "$path/$mbox", "$bkup/$mbox";
    system( "perl -ne 'print if /^From/..-1' $bkup/$mbox > $path/$mbox
+" );
}