As my dissertation draft grows bigger (and messier…), I see that I need to restrict the depth of the Table of Contents. These lines do the trick:

\setcounter{tocdepth}{1}
\tableofcontents

First I tried to use tocdepth 2, but that gave me three levels. I guess this is because it counts the chapter level as 0.

I have also been wondering why the bibliography hasn’t shown up in the table of contents. I haven’t found an explanation, but the solution is this:

\addcontentsline{toc}{chapter}{References}
\bibliographystyle{chicago}
\bibliography{arj-references}