warning: Harlowe isn't designed to play well with JavaScript.
1. Preparing your project's Story Javascript area.
The Baffle JavaScript library makes certain assumptions that are not correct for a HTML file built using Twine, to over come this fact you will need to add the following code to your project's Story Javascript area.
(function (define){
/* The Baffle library's source code will go here! */
}).call(window);
2. Adding the Baffle library source code to your project's Story Javascript area.
The Baffle web-site (you linked to) has a Download button, which when selected should show the contents of a baffle.min.js named JS file. You need to highlight and that contents and then paste it into the code from point 1 so that it appears between the line that reads (function (define){ and the line that reads }).call(window);
If everything was done correctly you should now have access to a baffle() JavaScript function.
3. Using the baffle() and related functions within a Passage.
As stated before Harlowe has limited support for using JavaScript within a project, the following example (based on those on the Baffle web-site) shows one method of using a <script> HTML element within a (link:) to call the once() function on a HTML element that has been assigned a demo-text CSS class.
<div class="demo-text js-demo">The quick brown fox jumps over the lazy dog.</div>
(link: "Once")[{
<script>
var b = baffle('.demo-text');
b.once();
</script>
}]