Hi Jon,
Thanks for the reply.

In this specific instance, I'm trying to add a JS/CSS files so that they're included on every page of my instance, regardless of whether or not my module is actually doing anything else. Testing shows it's only active under some circumstances, like I'm doing something with the footer, rendering a webpart, etc. Using the link you provided, they're not always included, for example, when I'm managing a data set. I tried adding them as <script> and <link> in a _footer but the page appears to try to render before the files are included, leading to a bunch of x is not defined errors or styles that aren't actually applied.

The last question was referring to the HomeTemplate files under /server/api/src/org/labkey/api/view/template/. In other tools there are master pages, templates, etc. that define the site-wide look. I was wondering if there was such a class or template I could touch, override, extend, etc. as a way to get the JS and CSS included in the manner I need.