In Joomla its very easy to edit the index.php file and to add your custom affiliate code or statcounter code. Navigate to Site---Template Manager---Site Templates

Here you will see a list of templates installed in your joomla website. You should be seeing the assigned and default template you are presently using. Checkbox it, and on the right top you will see written, Edit html, clicking this would direct you to the index.php file where you can edit or add.

Make sure you you dont delete anything there, unless you are sure what you are doing is right.

After you edit, click on SAVE you see on the top.

 This is how easy it is to edit or manage your index.php file.

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