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Hi,
JA Puresite is based on old JAT3v2 framework and it will not automatically load custom.css file as the new T3 framework, you need to call it via head block of this template
You can go to file: /templates/your_template_name/tpls/blocks/head.php
Add this line of code:
<link rel=”stylesheet” href=”templates/<?php echo T3_ACTIVE_TEMPLATE; ?>/css/custom.css” type=”text/css” />
Let me know if this helps