When a version 5.4 or 6.0 is released, that code will execute the set_magic_quotes_runtime function again, and we’ll be forced to change the code again.
But didnt you say that if the server doesnt support them CI will automatically rewrite them?
From the link above to the user guide:
Automatic Short Tag Support
Note: If you find that the syntax described in this page does not work on your server it might be that “short tags” are disabled in your PHP ini file. CodeIgniter will optionally rewrite short tags on-the-fly, allowing you to use that syntax even if your server doesn’t support it. This feature can be enabled in your config/config.php file.
I think a new topic would be best, with some additional context, i.e. what version of CI you’re running, where that code is located, the surrounding code, etc.