8 files changed, 137 insertions, 56 deletions
diff --git a/Master/texmf-dist/doc/latex/msu-thesis/README b/Master/texmf-dist/doc/latex/msu-thesis/README
index 60f22a62b24..06b9fc6043b 100644
--- a/Master/texmf-dist/doc/latex/msu-thesis/README
+++ b/Master/texmf-dist/doc/latex/msu-thesis/README
@@ -1,10 +1,10 @@
-MSU Thesis Class Version 2.4 2013/05/02
+MSU Thesis Class Version 2.5 2014/08/08
 
-Copyright 2011,2012,2013 by Alan Munn <amunn@msu.edu>
+Copyright 2011,2012,2013,2014 by Alan Munn <amunn@msu.edu>
 
 This is a class file for producing dissertations and theses according to
 the Michigan State University Graduate School Guidelines for Electronic
-Submission of Master's Theses and Dissertations (2013).
+Submission of Master's Theses and Dissertations (2014).
 
 The class is based on the memoir document class, and thefore inherits
 all of the functionality of that class.
diff --git a/Master/texmf-dist/doc/latex/msu-thesis/msu-thesis.pdf b/Master/texmf-dist/doc/latex/msu-thesis/msu-thesis.pdf
index d2db31546b9..f912e7c248f 100644
--- a/Master/texmf-dist/doc/latex/msu-thesis/msu-thesis.pdf
+++ b/Master/texmf-dist/doc/latex/msu-thesis/msu-thesis.pdf
diff --git a/Master/texmf-dist/doc/latex/msu-thesis/msu-thesis.tex b/Master/texmf-dist/doc/latex/msu-thesis/msu-thesis.tex
index e285e46603a..72f17bc83f1 100644
--- a/Master/texmf-dist/doc/latex/msu-thesis/msu-thesis.tex
+++ b/Master/texmf-dist/doc/latex/msu-thesis/msu-thesis.tex
@@ -3,7 +3,7 @@
 \documentclass[11pt]{article}
 \title{\textbf{Using the MSU Thesis Class}}
 \author{\textbf{Alan Munn}\\Department of Linguistics and Languages\\\texttt{\href{mailto:amunn@msu.edu}{amunn@msu.edu}}}
-\date{Version 2.4\\Aug 4, 2014}
+\date{Version 2.5\\Aug 8, 2014}
 \usepackage[T1]{fontenc}
 \usepackage[lmargin=1.25in,rmargin=1.25in,tmargin=1in,bmargin=1in]{geometry}
 \usepackage{titling}
@@ -66,7 +66,7 @@
 \thispagestyle{empty}
 \renewcommand{\abstractname}{\sffamily Abstract}
 
-\abstract{\noindent\begin{quote} This is a class file for MSU theses and dissertations.  It is based on the \pkg{memoir} class, and therefore supports all of the functionality of that class.  It should generate a document which meets all the basic formatting requirements laid out by the \emph{Formatting Guide For Submission of Master’s Theses and Doctoral Dissertations} (2013) produced by the Graduate School, including requirements for margins, titlepage, page numbering, section titles, sub- and superscript sizes etc.\end{quote}}
+\abstract{\noindent\begin{quote} This is a class file for MSU theses and dissertations.  It is based on the \pkg{memoir} class, and therefore supports all of the functionality of that class.  It should generate a document which meets all the basic formatting requirements laid out by the \emph{Formatting Guide For Submission of Master’s Theses and Doctoral Dissertations} (2014) produced by the Graduate School, including requirements for margins, titlepage, page numbering, section titles, sub- and superscript sizes etc.\end{quote}}
 \section{Introduction}
 Formatting a dissertation according to a University's thesis requirements is not always a simple task in \LaTeX, especially since the requirements are generally aimed at MSWord users.  Furthermore, most of the work of formatting a document is supposed to be done by the documentclass itself, and not by the individual user.  Fortunately, Michigan State University's thesis requirements are actually sane, and fairly straightforward.  The present class file is designed to further make the process easier for \LaTeX\ users, by doing all the heavy lifting for you, so that you can focus on the content and not the formatting.
 \section{Background}
@@ -98,8 +98,8 @@ In addition to any options passed to the \pkg{memoir} class (e.g. |oldfontcomman
 \end{table}
 \subsection{The \pkg{[lscape]} option}
 The Formatting Guide requires that any lansdscape pages be numbered in landscape mode (i.e. along the long edge of the page) rather than in portrait mode, and rotated in the final PDF. The |[lscape]| option enables this. The option loads both the \pkg{pdflscape} package and \pkg{tikz}, and is implemented as a class option so that you are not required to load those packages if they are not needed.
-\subsection{The \pkg{[noboldtoc]} option}
-In 2013 I received reports that the thesis office now requires all elements in the Table of Contents to have the same formatting as they are in the main document, which means that all section, subsection, and subsubsection headings need to be bold.  Since this looks very ugly, I have created an option to turn it off, the |[noboldtoc]| option. I suspect that the thesis office checkers don't notice this all the time so if you want to have a prettier table of contents and are willing to have that format be corrected, you can use this option to turn off the MSWord inspired ugliness of an entirely bold Table of Contents. Unfortunately, to comply with the standards, I've left the Table of Contents bold by default.
+\subsection{The contents options}
+In 2013 I received reports that the thesis office now requires all elements in the Table of Contents to have the same formatting as they are in the main document, which means that all section, subsection, and subsubsection headings need to be bold.  Since this looks very ugly, I have created two options to turn it off, the |[plaintoc]| option (which makes all TOC entries plain) and |[mixedtoc]| option (which makes Chapters bold and other elements plain). I suspect that the thesis office checkers don't notice this all the time so if you want to have a prettier table of contents and are willing to have that format be corrected, you can use these options to turn off the MSWord inspired ugliness of an entirely bold Table of Contents. I've made |[plaintoc]| the default.  If you are forced by the thesis office to have an entirely bold TOC, use the |[boldtoc]| option.
 \section{User commands}
 In addition to all the user functionality defined by \pkg{memoir}, the \pkg{msu-thesis} class defines six new titling commands, and a command to signal that the document has multiple appendices. 
 \begin{quote}
@@ -112,8 +112,8 @@ In addition to all the user functionality defined by \pkg{memoir}, the \pkg{msu-
 %\item[\texttt{\bs maketableofcontents}] Creates the table of contents
 %\item[\texttt{\bs begin\{msuabstract\}\ldots \bs end\{msuabstract\}}] Environment containing the text of the thesis abstract.
 %\item[\texttt{\bs makeabstract}] Generates the abstract.
-\item[\texttt{\bs appendicestrue}] Tells the class that you have more than one appendix.
-\item[\texttt{\bs makeappendixcover}] Creates the appendix/ces cover page.
+\item[\texttt{\bs appendix}] Tells the class that you have one appendix.
+\item[\texttt{\bs appendices}] Tells the class that you have more than one appendix.
 \item[\texttt{\bs makebibliographycover}] Creates the bibliography cover page.
 \end{description}
 \end{quote}
@@ -194,11 +194,12 @@ I have created a basic looking style for Chapter headings based on the |thatcher
 Despite there being no explicit formatting requirements for Chapter headings (other than that they start 1 in from the top of the page), the thesis office has been known to dislike many things, so if you do decide to change things, be prepared for rejection or a frustrating fight.
 \subsection{Things to watch out for}
 \begin{itemize}[label={\textbullet}]
+\item If you are having problems with the Thesis office about non-conforming formatting, please check first whether you have a local copy of the class instead of the latest version distributed via CTAN.
 \item If your title is long and you want to put a newline (|\\|) into it to improve the spacing, you must precede the newline with |\protect|.
 \item Make sure you pay attention to any ``Overfull hbox'' warnings when you are producing your final copy. You should make sure you eliminate all of them or else the thesis office is likely to reject your thesis. One common way to eliminate such warnings is to place the command |\sloppy| at the beginning of the paragraph that triggers the warning. You should only use this technique at the very end when you are completely done with everything.  Alternatively, rewording the text may also fix things. 
 \item Remember to use the |\tableofcontents*| command so that your table of contents is not listed in the table of contents.
-\item Remember to use the command |\appendicestrue| if you have more than one appendix.
-\item Remember to add the |\makeappedixcover| and |\makebibliographycover| commands before your appendices and your bibliography.
+\item Remember to use the command |\appendices| instead of |\appendix| if you have more than one appendix.
+\item Remember to add the |\makebibliographycover| command before your bibliography.
 \end{itemize}
 
 \section{Bugs and redistribution}
@@ -207,7 +208,7 @@ The latest copy of \pkg{msu-thesis} will always be available on  \href{http://tu
 \subsection{Archiving your thesis for the future}
 Since the current version of the \pkg{msu-thesis} class satisfies the Graduate School requirements at any one time, as these requirements change, you may find that if you need to recompile your thesis after you have graduated that the formatting changes. To avoid this, I would recommend saving an archived version of the \pkg{msu-thesis.cls} file in the same folder as your thesis file.  You only need to do this once you have completely finished your thesis however; there's no need to do it during the writing process. 
 \subsection{Version history}
-Previous versions of \pkg{msu-thesis} (versions 1.0--1.4b) were created for non-electronic submission and should not be used. Versions 1.5--1.6 (the first electronic submission versions) contained a |\makeabstract| command and a separate |msuabstract| environment. These have been removed as of version 1.7.  Users who are upgrading from earlier versions to version 1.7 do not need to change these commands however but their use will trigger a warning.) Version 2.0 implemented landscape pages; version 2.1 added limited support for \pkg{hyperref} although this is for convenience only at the moment. It's not clear what the Grad School policy is on hyperlinks in submitted theses.
+Previous versions of \pkg{msu-thesis} (versions 1.0--1.4b) were created for non-electronic submission and should not be used. Versions 1.5--1.6 (the first electronic submission versions) contained a |\makeabstract| command and a separate |msuabstract| environment. These have been removed as of version 1.7.  Users who are upgrading from earlier versions to version 1.7 do not need to change these commands however but their use will trigger a warning.) Version 2.0 implemented landscape pages; version 2.1 added support for \pkg{hyperref}. Versions 2.2--2.5 mainly accommodated to the ever changing whims of the MSU Graduate School. 
 \section{Acknowledgements}
 Thanks to Lars Madsen, Ulrike Fischer and Peter Wilson for help with setting up parts of the memoir code for versions 1.0-1.4 (now eliminated due to changed requirements). Thanks to Wolfgang Sternefeld for supplying the \pkg{linguex} spacing fix code, Leo Liu for the landscape page numbering code, which greatly simplified my original version, and Florent Chervet for the hyperref code. Thanks also to the following students who have reported problems over the years: Matt Husband, Irina Agafonova, Dmitriy Bryndin, Greg Christian, Changkuk Jung, Yisu Zhou, Neil ver Planck, Michael Wojcik and Kyle Crayne.
 
@@ -215,6 +216,7 @@ Thanks to Lars Madsen, Ulrike Fischer and Peter Wilson for help with setting up
 \renewcommand{\thesection}{Appendix \Alph{section}}
 \clearpage
 \section{Sample template}
+You can find a copy of this template \href{http://mirrors.ctan.org/macros/latex/contrib/msu-thesis/samples/MSU-thesis-template.tex}{here}.
 \enlargethispage{2\baselineskip}
 \begin{lstlisting}
 \documentclass[PhD]{msu-thesis} 
@@ -226,7 +228,7 @@ Thanks to Lars Madsen, Ulrike Fischer and Peter Wilson for help with setting up
 \author{Joe Linguist}
 \fieldofstudy{Linguistics} % should be in sentence case
 \dedication{This thesis is dedicated to someone.}
-\date{2009}
+\date{2014}
 %
 \begin{document}
 \frontmatter
@@ -258,7 +260,6 @@ Your acknowledgements here
 \chapter{Your first chapter}
 %
 \appendix
-\makeappendixcover
 \chapter{Your first appendix}
 \backmatter
 \makebibliographycover
@@ -269,18 +270,16 @@ Your acknowledgements here
 \end{lstlisting}
 \clearpage
 \section{Linguistic Examples with \pkg{gb4e} and \pkg{linguex}}
-The \pkg{msu-thesis} class has been tested with both the \pkg{gb4e} package, and the \pkg{linguex} package.  Unfortunately some versions of \pkg{gb4e} use old font commands, and so does \pkg{linguex}, so if you encounter problems with either package, load the class with the |oldfontcommands| option. Since linguistic examples are usually single spaced, even in theses, you should use the |\singlegloss| command (from the \pkg{cgloss4e} package loaded by both \pkg{gb4e} and \pkg{linguex}) to make your glosses examples singlespaced.  The default mode for examples themselves is to make them doublespaced. If you want all examples to be single spaced (which looks better if the examples take up more than one line) you need to put the following code in your preamble, which redefines the |exe| environment to be single spaced.
+The \pkg{msu-thesis} class has been tested with both the \pkg{gb4e} package, and the \pkg{linguex} package.  Unfortunately some versions of \pkg{gb4e} use old font commands, and so does \pkg{linguex}, so if you encounter problems with either package, load the class with the |oldfontcommands| option. Since linguistic examples are usually single spaced, even in theses, you should use the |\singlegloss| command (from the \pkg{cgloss4e} package loaded by both \pkg{gb4e} and \pkg{linguex}) to make your glosses examples singlespaced.  The default mode for examples themselves is to make them doublespaced. If you want all examples to be single spaced (which looks better if the examples take up more than one line) you need to put the following code in your preamble, which redefines the |exe| environment to be single spaced. The |\patchcommand| macro is part of \pkg{memoir}. Other patching commands such as those provided by the \pkg{etoolbox} package could also be used.
 \begin{quote}
 \begin{lstlisting}
-\let\oldexe\exe
-\renewcommand{\exe}{\SingleSpacing\oldexe}
+\patchcommand{\exe}{\SingleSpacing}{}
 \end{lstlisting}
 \end{quote}
 For the \pkg{linguex} package, you can use the following code:
 \begin{quote}
 \begin{lstlisting}
-\let\oldex\ex
-\renewcommand{\ex}{\SingleSpacing\oldex}
+\patchcommand{\ex}{\SingleSpacing}{}
 \renewcommand{\ExEnd}{%
     \ifnum\theExDepth=0\global\unembeddedfalse\DoubleSpacing\else%
 	  \end{list}\addtocounter{ExDepth}{-1}\ExEnd\fi}
diff --git a/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-template.pdf b/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-template.pdf
index d7f3e8638ce..a83cd3722be 100644
--- a/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-template.pdf
+++ b/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-template.pdf
diff --git a/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-template.tex b/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-template.tex
index 8eed362a718..e9bbaf44011 100644
--- a/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-template.tex
+++ b/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-template.tex
@@ -22,7 +22,12 @@
 % Just add real content and you're done!
 %
 \documentclass[]{msu-thesis}
-% for a prettier, but possibly non-compliant table of contents use the [noboldtoc] option
+%
+% for a prettier, but possibly non-compliant table of contents use the [mixedtoc] option
+% for a plain table of contents use the [plaintoc] option
+% for a horrendous looking, but possibly required table of contents, use the [boldtoc] option
+%
+% If you have large tables/figures that need to be in landscape mode, add the [lscape] option
 
 % This is standard fontenc/inputenc for pdflatex
 % If you use LuaLaTeX or XeLaTeX you should replace this with the fontspec package
@@ -31,7 +36,7 @@
 %
 % If the thesis office requires Times, we'll give them Times
 % You can experiment with other font packages here if you like.
-% If you are using XeLaTeX or LuaLaTeX load the Times or Times New Romaan font with \setmainfont
+% If you are using XeLaTeX or LuaLaTeX load the Times or Times New Roman font with \setmainfont
 \usepackage{mathptmx} 
 %
 % Load any extra packages here
@@ -40,7 +45,7 @@
 \title{The syntax and semantics of phonology}
 \author{Joe Linguist}
 \fieldofstudy{Linguistics} % This should be in sentence case
-\date{2013}
+\date{2014}
 
 % If you want a dedication page, specify the text of the dedication here and uncomment the next command.
 %
@@ -63,7 +68,7 @@
 % from having a copyright page unless you pay ProQuest to register the copyright.
 % This should be illegal, but I didn't make up the rule.
 
-%\makecopyrightpage
+\makecopyrightpage
 
 % If you have a dedication page, uncomment the next command to print the dedication page
 %
@@ -107,9 +112,9 @@ Your acknowledgements here.
 %
 % If you have appendices, they would go here.  
 % Comment these lines out if you don't
-% If you have more than one appendix, uncomment the next line
-%\appendicestrue
-\makeappendixcover % make the appendix cover page
+% If you have more than one appendix, uncomment the next line and comment out the \appendix line
+%
+%\appendices
 \appendix
 \chapter{Your first appendix}
 %
diff --git a/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-testfile.pdf b/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-testfile.pdf
index 3964ee1ab57..2565efc84f0 100644
--- a/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-testfile.pdf
+++ b/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-testfile.pdf
diff --git a/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-testfile.tex b/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-testfile.tex
index 8e22deaa245..18516c337a0 100644
--- a/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-testfile.tex
+++ b/Master/texmf-dist/doc/latex/msu-thesis/samples/MSU-thesis-testfile.tex
@@ -1,6 +1,7 @@
+% !BIB TS-program = bibtex
 \listfiles
 
-\documentclass[lscape]{msu-thesis}
+\documentclass[lscape,plaintoc]{msu-thesis}
 % lscape option is needed for this sample file to show correct placement
 % of page numbers on landscape pages. If you don't have any landscape pages
 % in your document, you don't need to load this option.
@@ -12,23 +13,22 @@
 \author{Joe Linguist}
 \fieldofstudy{Linguistics}
 \dedication{This thesis is dedicated to someone.}
-\date{2010}
+\date{2014}
 
 \usepackage{lipsum}
-\usepackage[T1]{fontenc}
 \usepackage{xcolor}
 \usepackage{gb4e}
 \usepackage{cgloss}
 \usepackage{natbib}
+\usepackage{hyperref} % not needed but here for testing
 
 
 
 \counterwithin{exx}{chapter}
 \bibliographystyle{unified}
 \singlegloss
-% Uncomment the next two lines for single spaced examples with gb4e
-%\let\oldexe\exe
-%\renewcommand{\exe}{\SingleSpacing\oldexe}
+% Uncomment the next line for single spaced examples with gb4e
+%\patchcommand{\exe}{\SingleSpacing}{}
 
 
 
@@ -193,13 +193,17 @@ A & B & C & D & E & F & G \\
 % at the end of the {landscape} environment, make the page style {plain}
 \pagestyle{plain}
 %
-% Uncomment this next command if you have more than one appendix
-%\appendicestrue
-% This command creates the cover page for the appendix/appendices
-\makeappendixcover
-\appendix
+
+
+\appendices  % use this if you have more than one appendix
+%\appendix   % use this if you have only one appendix
+
 \chapter{An appendix}
+\section{An appendix section}
 \lipsum[9-15]
+\chapter{An second appendix}
+\section{An appendix section}
+\lipsum[16-17]
 \backmatter
 % The next command forces the Bibliography to have a dotted leader
 % (May not be required)
diff --git a/Master/texmf-dist/tex/latex/msu-thesis/msu-thesis.cls b/Master/texmf-dist/tex/latex/msu-thesis/msu-thesis.cls
index 41ef4488da9..d2c2a85f9a2 100644
--- a/Master/texmf-dist/tex/latex/msu-thesis/msu-thesis.cls
+++ b/Master/texmf-dist/tex/latex/msu-thesis/msu-thesis.cls
@@ -84,8 +84,8 @@
 % Version 2.1d 2012/05/27 Removed superfluous title redefinition;
 %                         Made title in abstract upper case (bug);
 %                         Updated documentation; updated degree list
-% Version 2.2 2012/06/07	Made changes to case of copyright page and program name
-%												as per user report.  Who knows if the grad school will
+% Version 2.2 2012/06/07 Made changes to case of copyright page and program name
+%						 as per user report.  Who knows if the grad school will
 %                        change their mind again.  What kind of people care about this?
 %                        Name on copyright page is now upper case;
 %                        Program name is now as typed.
@@ -102,14 +102,25 @@
 %                        are bold; this can be turned off with the [noboldtoc] option for a 
 %                        prettier, but possibly non-compliant TOC.
 %						 Changed capitalization of 'by' to 'By' which makes things so much better...
+% Version 2.5 2014/08/08 Fixed problem with bibliography cover page and appendix formatting
+%						 Bibliography cover page is now the page that appears in the TOC
+%                        Different TOC format for 1 or >1 appendices
+%                        User commands simplified: \appendix = 1 appendix; \appendices = >1
+%						 Added three TOC options: boldtoc, plaintoc, mixedtoc replacing noboldtoc
+%						 Improved hyperref support for Appendices and Bibliography
 %                    
 % Use at your own risk! 
 % Report bugs/problems/questions to <amunn@msu.edu>
 %
+\def\msu@version{2.5}
+\def\msu@date{2014/08/08}
 \NeedsTeXFormat{LaTeX2e}
-\ProvidesClass{msu-thesis}[2014/08/04  Michigan State University Thesis Class version 2.4]
+\ProvidesClass{msu-thesis}[\msu@date  Michigan State University Thesis Class version \msu@version]
 \newif\ifmsu@lscape\msu@lscapefalse
-\newif\ifmsu@stupid\msu@stupidtrue
+\newif\ifmsu@stupidtoc\msu@stupidtocfalse
+\newif\ifmsu@mixedtoc\msu@mixedtocfalse
+\newif\ifmsu@plaintoc\msu@plaintoctrue % make this the default to see what the reaction is
+\newif\ifmsu@hyperloaded\msu@hyperloadedfalse
 \DeclareOption{PhD}{\gdef\@degree{Doctor of Philosophy}\gdef\@diss{DISSERTATION}}
 \DeclareOption{MA}{\gdef\@degree{Master of Arts}\gdef\@diss{THESIS}}
 \DeclareOption{MS}{\gdef\@degree{Master of Science}\gdef\@diss{THESIS}}
@@ -125,7 +136,9 @@
 \DeclareOption{lscape}{%
 \msu@lscapetrue
 \AtEndDocument{\ClassWarningNoLine{msu-thesis}{You have chosen the [lscape] option. You may need to run latex twice to get landscape page numbering to display correctly}}}
-\DeclareOption{noboldtoc}{\msu@stupidfalse}
+\DeclareOption{boldtoc}{\msu@stupidtoctrue\msu@plaintocfalse\msu@mixedtocfalse}
+\DeclareOption{plaintoc}{\msu@plaintoctrue\msu@stupidtocfalse\msu@mixedtocfalse}
+\DeclareOption{mixedtoc}{\msu@mixedtoctrue\msu@stupidtocfalse\msu@plaintocfalse}
 \ExecuteOptions{PhD}
 \DeclareOption*{% 
 \PassOptionsToClass{\CurrentOption}{memoir}% 
@@ -172,13 +185,12 @@
 % polyglossia if they are loaded since they redefine the contents title
 % 
 \newcommand*\msu@contentsname{TABLE OF CONTENTS} 
-  
+
 \newif\ifappendices\appendicesfalse
 \newcommand*{\@appendixcover}{\ifappendices{APPENDICES}\else{APPENDIX}\fi}
 \newcommand*{\fieldofstudy}[1]{\gdef\@fieldofstudy{#1}} % removed \MakeUppercase 6/5/12
 \newcommand{\dedication}[1]{\gdef\@dedication{#1}}
 \newcommand*{\degree}[1]{\gdef\@degree{\MakeUppercase{#1}}}
-\newcommand*{\appendixcover}[1]{\gdef\@appendixcover{\MakeUppercase{#1}}}
 
 % msuabstract environment (not needed now) but included for backwards 
 % compatibility
@@ -230,15 +242,37 @@
 \renewcommand*{\cfttablename}{Table\space}
 
 % Stupid option to make the TOC all bold
-\ifmsu@stupid
-\renewcommand*{\cftsectionfont}{\bfseries}
-\renewcommand*{\cftsubsectionfont}{\bfseries}
-\renewcommand*{\cftsubsubsectionfont}{\bfseries}\fi
+\ifmsu@stupidtoc
+	\def\msu@tocfont{\bfseries}
+	\def\msu@chapfont{\bfseries}
+\fi
+\ifmsu@plaintoc
+	\def\msu@tocfont{\normalfont}
+	\def\msu@chapfont{\normalfont}
+
+\fi
+\ifmsu@mixedtoc
+	\def\msu@tocfont{\normalfont}
+	\def\msu@chapfont{\bfseries}
+
+\fi
+
+\renewcommand*{\cftchapterfont}{\msu@chapfont}
+\renewcommand*{\cftchapterpagefont}{\msu@chapfont}
+\renewcommand*{\cftsectionfont}{\msu@tocfont}
+\renewcommand*{\cftsubsectionfont}{\msu@tocfont}
+\renewcommand*{\cftsubsubsectionfont}{\msu@tocfont}
+\renewcommand*{\cftsectionpagefont}{\msu@tocfont}
+\renewcommand*{\cftsubsectionpagefont}{\msu@tocfont}
+\renewcommand*{\cftsubsubsectionpagefont}{\msu@tocfont}
 
 \renewcommand*{\l@chapter}[2]{%
+  \renewcommand{\cftchapterpagefont}{\msu@chapfont}
   \l@chapapp{\MakeUppercase{#1}}{#2}{\cftchaptername}} % Format chapter names
 \renewcommand*{\l@appendix}[2]{%
-  \l@chapapp{\MakeUppercase{#1}}{#2}{\cftappendixname}} % Format appendix names
+ \renewcommand{\cftchapterpagefont}{\msu@tocfont}
+  \setlength{\cftchapternumwidth}{2em}
+  \l@chapapp{\msu@tocfont{#1}}{#2}{\cftappendixname}} % Format appendix names
 \setlength{\cftchapternumwidth}{3em}
 \setrmarg{3.5em} % better wrapping of long titles
 %\setlength{\cftbeforechapterskip}{1.0em \@plus\p@}
@@ -314,36 +348,75 @@
   \DoubleSpacing\pagestyle{plain}\@ifstar{\@smemmain}{\@memmain}}
 
 
+
 % make the appendices cover page
-\newcommand*{\makeappendixcover}{%
+% Two new commands added \appendix and \appendices
+% no longer need to set switch manually
+% added 8/7/14
+
+\newcommand*{\@makeappendixcover}{%
+\addcontentsline{toc}{chapter}{\@appendixcover}
+\ifappendices  
+   \settocdepth{chapter}
+   \addtocontents{toc}{%
+      \setlength{\cftchapterindent}{1.5em}
+      \setlength{\cftbeforechapterskip}{0.0em \@plus\p@}
+}
+\else
+   \settocdepth{part}
+\fi
 \clearpage
 \chapter*{\ }
 \vspace{.35\textheight}\begin{center}
 \bfseries\@appendixcover
-\end{center}}
+\end{center}
+\ifmsu@hyperloaded
+	\renewcommand{\theHchapter}{A\arabic{chapter}}
+\fi
+}
+\let\orig@appendix\appendix
+\let\orig@appendices\appendices
+\let\orig@endappendices\endappendices
+\renewcommand*{\appendix}{\appendicesfalse\@makeappendixcover\orig@appendix}
+\renewcommand*{\appendices}{\appendicestrue\@makeappendixcover\orig@appendix}
+\renewcommand*{\endappendices}{}
 
 % make the bibliography page
+% Modified 8/7/14 to add the bibliography cover page to the TOC and not the actual bibliography page
+% This should also work for biblatex even though memoir doesn't check for it
+% but we'll worry about that when someone asks...
 \newcommand*{\makebibliographycover}{%
+\ifmsu@hyperloaded
+	\phantomsection\label{msu@bib}\fi
+\settocdepth{chapter}
+\addtocontents{toc}{
+	  \setlength{\cftchapterindent}{0em}
+      \setlength{\cftbeforechapterskip}{1.0em \@plus\p@}
+      }
+\addcontentsline{toc}{chapter}{BIBLIOGRAPHY} % put the title page in the TOC
+\nobibintoc % remove the actual bib first page from the TOC
 \clearpage
-\chapter*{\ }
+\chapter*{\ } % this is a hack but it works
 \vspace{.35\textheight}\begin{center}
 \bfseries\MakeUppercase{\bibname}
-\end{center}}
+\end{center}
+}
 
 % Do some stuff at begin document: check for hyperref
 % The hyperref code allows hyperref to be used. It is not guaranteed to 
-% work, and the thesis office presumably doesn't allow hyperlinks.
+% work and has been lightly tested
 % If the thesis office permits them, then I may try to support this more.
 % Thanks to Florent Chervet for the code.
 \AtBeginDocument{%
 \@ifpackageloaded{hyperref}%
-{\def\MakeLinkUppercase \hyper@linkstart #1#2#3\hyper@linkend
+{\msu@hyperloadedtrue
+	\def\MakeLinkUppercase \hyper@linkstart #1#2#3\hyper@linkend
           {\hyper@linkstart {#1}{#2}{\MakeUppercase{#3}}\hyper@linkend }
 \pdfstringdefDisableCommands{\let\MakeUppercase \@firstofone }
 \renewcommand*{\l@chapter}[2]{%
    \l@chapapp{\MakeLinkUppercase #1}{#2}{\cftchaptername}} % Format chapter names
 \renewcommand*{\l@appendix}[2]{%
-  \l@chapapp{\MakeLinkUppercase #1}{#2}{\cftappendixname}}} % Format appendix names
+  \l@chapapp{\msu@tocfont#1}{#2}{\cftappendixname}}} % Format appendix names (changed 8/7/14)
 % if no hyperref
 {\relax}}
 \endinput
 \ No newline at end of file