Keep in mind that when using ssh2_shell, the remote system's EOL may not be the same as PHP's EOL, so it may not be safe to use PHP_EOL. The native EOL for Windows is \r\n, while Unix is typically merely \n, and classic Mac for some reason is \r.
If you're running PHP on Windows (\r\n) and sshing into a Unix box (\n) you're going to end up sending extra lines. My experience so far is that it just acts as though you typed nothing, which may cause issues with password prompts.
Oh, and \n\r? Don't do that. Nobody does that.
