WordPress.org

1. Upload wp-js folder to the /wp-content/plugins/ directory
2. Activate the plugin through the 'Plugins' menu in WordPress
3. Set the permissions for /wp-js/ folder to 777
4. Go to Settings > WP JS in the admin site. This setup the plugin.
5. Use <?php wp_js('path/to/js/file.js'); ?> to link to your JavaScript file.

i.e. <script src="<?php wp_js('path/to/js/file.js'); ?>" type="text/javascript"></script>