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I uploaded a few .js files, so my js folder is in the root (The same level as wp-contents). I have a few .js files, but I just uploaded the masonry library and when I try to access it via domain.com/js/masory.js, it just goes to a 404. Is there something I am supposed to do with Wordpress ? The weird thing is, my other javascript in the same file works and it doesn't go to the 404.

For example, my custom.js (jQuery stuff) works, but the other doesn't:

<script language="javascript" type="text/javascript" src="http://domain.com/js/jquery.eachdelay-0.0.1.js"></script>
<script language="javascript" type="text/javascript" src="http://domain.com/js/jquery.masonry.min.js"></script>
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you should place your Javascript files in a subfolder of your theme rather than adding folders to the base structure of WP.

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What I usually do is create a folder for the scripts inside the theme folder then place this line to the header.php

<script language="javascript" type="text/javascript" src="<?php bloginfo('template_directory'); ?>/scriptsfolder/script.js"></script>
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