Oops, I have just discovered that there wasn't any wait_eof method. The function libssh2_channel_wait_eof was not being wrapped by Net::SSH2.

Also, unfortunately, wait_closed fails unless the channel is already at EOF.

My advice is to get the new version 0.59_16 which I have just uploaded to CPAN and providing wait_eof and use it as follows:

my $chan = $ssh->channel();
$chan->ext_data('merge');
$chan->shell();
print $chan <<EOS;
cd /tmp
dbcfg_export -o /tmp/$filename.cfg -p '$pwdfile'
tar -C /usr/local/cdcs -zcvf - ipsec.d openvpn-keys ssh-hostkeys \\
    | openssl des3 -salt -k '$pwdfile' \\
    | dd of=/tmp/vpn.des3
tar -zcvf /opt/cdcs/upload/$filename.cfg.tar.gz $filename.cfg vpn.des3
EOS

$chan->send_eof;
print while (<$chan>);
$chan->wait_eof;
$chan->close;
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