There are some Lynda.com videos which offer detailed explanation on HTTP header and output buffering:
PHP with MySQL Essential Training - Modifying Headers, page redirection, and output buffering
You can turn on output buffering either on each php file, or you can do it in the php.ini. Only one way is required but you are free to do both.
Very often, you won't have access to your php.ini files on the server. You can modify all php files by doing the below:
at the beginning of all the php files, write
ob_start();
?>
at the very end of the php files, write
ob_end_flush();
?>
Bear in mind that if you do an include (anotherfile.php) in the index.php file, you might need to modify the file directories for the css, js, or whatever other files you have in the included php file, as this file is seeing the folder structure from the root level.
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