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The main file is the file called "thesis.tex". This is the main file that calls all of the other files; it's the only one you ever have to "run". It calls all of the other .tex files, and it automatically generates a PDF every time you run it. (To "run" or typeset the document in TeXworks, use CTRL+T or click on the green circle with the arrow in the top left of the screen.) For all the other .tex files, you just make changes in them, and then save. Then you run thesis.tex, and the changes will be reflected in the new PDF.
===thesis.tex===
The first big chunk of thesis.tex is all formatting stuff. You really don't have to change any of it, unless you want to add fancy new packages to get more features in the document. (I don't know how to do this.) One thing you can do is use the "Margin Check". If you comment out line 15 (\documentclass[12pt]{withesis}) using a %, and then uncomment line 18 (\documentclass[12pt,margincheck]{withesis}), then it will generate a PDF that has black boxes in the right margin anywhere where your document goes outside of the accepted margins.
For appendices, it is the same as chapters, except you use the \include command between the commands \begin{appendices} and \end{appendices}.
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The first chapter you'll want is call myprelude.tex. (You can change this file name or any other file name, as long as you change both the file name and the code that calls it.) The prelude is where you enter the title page info, the dedication, the acknowledgements, and the abstracts. It also generates the table of contents and the lists of tables and figures.
There are lots of things you can change in this file. I'll only mention the ones that I changed.
In the "TITLE PAGE" section, you enter the title, your name, and the date. You may want to play around with the spacing by adding vertical spaces if your title is multiple lines. (See below for vertical space command.)
You can edit the department (\department) if you're not in Physics, and you can enter your dedication and acknowledgements in those sections.
The CONTENTS, TABLES, FIGURES section doesn't have to be edited. It automatically generates a table of contents and a list of figures.
Enter your advisor name and title (\advisorname and \advisortitle), and then enter your abstract. For the abstract, you can either have a separate .tex file called abstract, which is called by \include abstract. (If you'd rather, you can comment out that line, and then uncomment the section below. You then type in your entire abstract in between the lines \begin{abstract} and \end{abstract}.)
===Chapter .tex files==
general chapter
\ref{}
\begin{equation, eqnarray}
\vspace
! between letters
\textit{
\text{
spelling
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