@frozenwithjoy, thanks for the reply. To answer your questions:

1. It doesn't seem that reversing the order of the commands

   print "$command\n";
   $exp->send("$command\n");
   

   makes any difference either to the STDOUT or logfile output. It still gives:

   (1) (2) Here is the second command
   error
   (3) Error on command #3
   (4) commit
   This is the last command
   Committing data
   (5) (6) exit
   Exiting program...
   

2. The server script has to print out the "(1) " before it receives any input. When it gets a line, it simply prints out "(2) " , waits for the next line, prints "(3) ", waits for the next line, etc. The code isn't optimized, but that's at least the explanation of why the $counter = 1 and the first print statement comes before the loop.

   That is, if you ran the server script and entered stuff, you'd get:

   (1) This is the first line I typed.  Now I'm hitting <ENTER>
   (2) I'm typing more stuff.
   (3) exit
   Exiting program...
   

3. Good question. The server script is actually representing what I cannot control in this. It may be a company-wide program I'm trying to interact with, or a Juniper router, or an IDS box, or probably a lot of other things. So unfortunately for this example I have to pretend that I can't modify the server's output. All I can do is interact with the (program, router, server, etc.) myself, see what it outputs when I interact with it manually, then try to reconstruct that exact output when my Expect.pm script interacts with the (program, router, server, etc.) in the same way.