Files are in one of two directories tex (for the tex files) and img (for
image files) directory which contains:
tex
├── acknowledgements.tex
├── bibliography.bib
├── frontcover.tex
├── main.tex
├── chapters
│ └── chapter1.tex
│ └── chapter2.tex
│ └── chapter3.tex
img
├── plot1.pdf
├── plot2.pdf
├── markov_chain.tex
├── universitylogo.eps
Compiling the main.tex file pulls in all the other files as required. The
chapter{1,2,3}.tex files would be where the main part of your content goes.
To read more about multi file LaTeX projects see this wiki
page.
In the img directory there are a combination of pdf and eps images as
well as a a tikz diagram (markov_chain.tex).
To handle all these files I recommend compiling with xelatex.