Why Doesn't the Composition Plugin Work with Custom Themes?

Add-on:Composition
Question:Why Doesn't the Composition Plugin Work with Custom Themes?
Answer:

Composition relies on some external javascript files which the default theme includes by for the label feature. If Composition tries to include those files itself manually, the rest of the page will break.

There is a <script> include within the labels include that you can simply put instead of the whole labels code, but essentially, you need the following in your theme somewhere:

<script type="text/javascript" src="[your webapp context]/includes/js/scriptaculous/lib/prototype.js"></script>
<script type="text/javascript" src="[your webapp context]/includes/js/scriptaculous/src/util.js"></script>
<script type="text/javascript" src="[your webapp context]/includes/js/scriptaculous/src/effects.js"></script>