CLI stands for "Command Line Interface" - it's what you're using when you login to the server remotely and execute commands.
The "-c <path>" argument is something you add after the program name (e.g. "/path/to/php -OPTION1 -OPTION2 -OPTION3" etc.). The <path> text is a placeholder for the path to the directory where the php.ini file is, such as /usr/local/opt/coolstack/php5/lib (according to your post above).
Like I said, you can also add this argument (I think, anyway) onto the "shebang" line in the .php file itself, e.g. this:
#!/usr/local/opt/coolstack/php5/lib
could instead be:
#!/usr/local/opt/coolstack/php5/php -c /usr/local/opt/coolstack/php5/lib
Also note that the path directly following the "#!" sequence should be the path to the file you want the shell to execute to parse the file. In this case, you should be supplying a path to the PHP executable file (I took a wild guess in my second code snippet above - you might have to fix the path), not a lib directory.
EDIT: In addition, note that the use of the "<?" short tags has been deprecated. These tags are disabled by default and even removed altogether from future versions of PHP, so you should make sure all of your scripts use the full "<?php" tag instead of the "<?" (or "<?=(expression)?>") syntax.
Oh, and by the way... I didn't know if you obfuscated them or not, so I removed the MySQL credentials you posted in the code snippet above. :p