Abstract File
Acknowledgements
Appendix

includes nice tables and image insertion code
Bibliography TeX file

You probably don't need to change this at all.
The real bibliography file
Ch1 Introduction
ch2 Background
ch3 Methodology
ch4 Analysis
ch5 Discussion
Chapter template, for making more
contents

you should not need to alter this file. Remember to run LaTeX twice to
populate data sources like this.
Cover Page

be sure to read your requirements document from your university and
department.
MAIN

Like any good piece of software, it all starts here.
texshop files

If you use texshop, these cause texshop to compile main.tex instead of
the chapter file. The chapter files won't build on their own.