All of the HTML is generated by PHP--there are no static HTML pages. If what you're displaying there is intended to be the public view of Collection Tree, it would (I think) be in yourtheme/collection-tree/index/index.php
You might want to take a look at one of the themes put out by CHNM (Thanks Roy, Berlin, Seasons) to get an idea of how themes are structured:
http://omeka.org/add-ons/themes/
You can read more about the technical details of themes (assuming you're using 2.x) at
http://omeka.readthedocs.org/en/latest/Tutorials/index.html#modifying-themes