With the latest version of Animate CC (15.1.1.13) you can edit the HTML template used for publishing easily.
In the "Publish Settings" go to "Advanced" and export the default template. Open the exported HTML file and inject any additional JavaScript libraries after <!-- write your code here -->
.
e.g. add <script src="http://code.jquery.com/jquery-2.2.3.min.js"></script>
to use jQuery.
After saving the HTML file go back to "Publish Settings" and import your modified template with "Import New...".
You can use this approach with your own libraries and relative paths, just make sure they are available in the directory of the output file (same as .fla by default).
e.g. <script src="foo.js"></script>