How to add plugin with jQuery to custom theme?

It should be said, that WordPress comes with jQuery out-of-the-box. You can check it, if you slap this in your page-template (based on this post):

window.onload = function() {
    if (window.jQuery) {  
        // jQuery is loaded  
        alert("Yeah!");
    } else {
        // jQuery is not loaded
        alert("Doesn't Work");
    }
}

In case you need other scripts, then perhaps look into the wp_enqueue_script-function.

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Only load script on certain pages

Based on your comment, then I thought I add a snippet you could try (from this page):

function custom_enqueue_scripts() {
  if ( is_page_template( 'page-template-name.php' ) ) {
    wp_enqueue_script( 'custom-script', get_stylesheet_directory_uri() . '/assets/js/YOUR_CUSTOM_SCRIPT.js', array( 'jquery' ) );
  }
}
add_action( 'wp_enqueue_scripts', 'custom_enqueue_scripts' );

As you can see, then the third parameter is array( jquery ), which is an array of dependencies. Which means that your script will not be loaded before that given script (jquery) has been loaded. Super-smart! 🙂

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Load script on all pages

This is if you want your script to load on all pages.

function custom_enqueue_scripts() {
    wp_enqueue_script( 'custom-script', get_stylesheet_directory_uri() . '/assets/js/YOUR_CUSTOM_SCRIPT.js', array( 'jquery' ) );
}
add_action( 'wp_enqueue_scripts', 'custom_enqueue_scripts' );