$hash{$msgid} = {
    filepos => $msgstart,
    inreply => $msgreply,
    nextmsg => []  # reference to an empty array
}

##</code><code>##

my @heads;
while(my ($key, $value) = each(%hash)) {
    # does this msg have a parent?
    if (my $parent = %hash{$value->{inreply}}) {
        # link the parent to this message
        push @{$parent->{nextmsg}}, $key;
    }
    else {
        # no parent so it must become a thread start
        push @heads, $key;
    }
}

##</code><code>##

foreach my $msgid (@heads) {
    # do what ever you have to do to start a new thread
   
    # recursively follow the messages
    thread_msgs($hash{$msgid});
}

# recursively read through the thread
sub thread_msgs {
    my $msgid = shift;

    # use seek() to position the mbox file at
    # the message start using $msgid->{filepos}
    # copy to the end of the message

    foreach $msgid (@{$msgid->{nextmsg}}) {
        thread_msgs($msgid);
    }
}