Using Javascript
Unless there’s a good reason to put them elsewhere, scripts should live in assets/js. In addition, scripts for epub output should be in _epub/js, as described below.
To add them to your <head> elements, add <script> tags to _includes/head-elements.
To add them just before the </body> tag, add <script> tags to _includes/end-elements.
You can also link to remote scripts here, without the need to place the actual scripts in the js folder.
Keep in mind that anything you add to head-elements will be added to all books in the project folder, and to all their formats.
Limiting scripts by book or format
To limit a script to a given book or format, wrap the script tag in Liquid control flow tags. For instance:
{% include metadata %}
{% if book-directory == "grapes-of-wrath" %}
<script src="{{ site.baseurl }}/assets/js/grapes-of-wrath.js"></script>
{% endif %}
(The include metadata tag fetches all kinds of information about the page, including which book-directory it’s in.)
To limit a script to a given output format, use site.output:
{% if site.output == "print-pdf" %}
<script src="{{ site.baseurl }}/assets/js/print-headers.js"></script>
{% endif %}
Adding scripts to epubs
Scripts in epub are special. While web and PDF scripts should be in /assets/js, all scripts to be used in your epub should be in _epub/js. This is because you must not have any scripts in your epub that you aren’t using, or it won’t validate. By keeping epub scripts separate, only your epub scripts will end up in the epub package.
Also, epub scripts must have a YAML frontmatter block, and use a layout with no HTML:
---
layout: min
---
This block tells Jekyll to process the script, which means it knows about it, which the epub packager needs in order to include it in the epub manifest.
Linking to scripts for epub
In the finished epub, these scripts will end up in a js folder alongside text, styles, images and fonts. So all links to scripts that you want to include in epub output should be in site.output == "epub" tags.
To ensure that links to scripts work from both parent-language and translation-language files, use the {{ path-to-book-directory }} tag in the path to the epub scripts:
{% if site.output == "epub" %}
<script src="{{ path-to-book-directory }}js/foo.js"></script>
{% endif %}