This project has the Thesis template for UPenn CIS students, that I got by modifying the template here. As far as I can tell by inspecting earlier theses before me, this template is correct.
I have organized chapters into folders so that all .tex files relevant to a certain chapter remain in one place.
I also have a makefile that compiles chapters separately (with bibliography), so that you can quickly compile the chapter you are working on, without compiling the entire thesis.
Ensure that the correct biblio setting is active,
%% TO TURN ON BIB FOR CHAPTER (when compiling chapters separately)
% \def\biblio{\bibliographystyle{abbrvnat}\bibliography{thesis}}
%% TO TURN OFF BIB FOR EACH CHAPTER, (for compiling the whole thesis)
\def\biblio{}And then run
make clean; make
To compile a single chapter for proofreading.
Ensure that the correct biblio setting is active,
%% TO TURN ON BIB FOR CHAPTER (when compiling chapters separately)
\def\biblio{\bibliographystyle{abbrvnat}\bibliography{thesis}}
%% TO TURN OFF BIB FOR EACH CHAPTER, (for compiling the whole thesis)
% \def\biblio{}And then run
make clean; make chapter1.pdf
Line numbers are useful for getting comments from people. Remove them for the final version by commenting out the following
% FOR ADDING LINE NO. I have checked, this does not mess with margins (i.e. the # appears outside the margins, so no new orphans/widows are introduced)
\usepackage{lineno}
\linenumbers