DVIPS warning messages and removed deprecated code

Acknowledgement/acknowledgement.tex

@@ -1,19 +1,9 @@
-% Thesis Acknowledgements ------------------------------------------------
+% ************************** Thesis Acknowledgements *****************************
 
-
-%\begin{acknowledgementslong} %uncommenting this line, gives a different acknowledgements heading
-\begin{acknowledgements}      %this creates the heading for the acknowlegments
+\begin{acknowledgements}      
 
 
 And I would like to acknowledge ...
 
 
 \end{acknowledgements}
-%\end{acknowledgmentslong}
-
-% ------------------------------------------------------------------------
-
-%%% Local Variables: 
-%%% mode: latex
-%%% TeX-master: "../thesis"
-%%% End: 

Appendix1/appendix1.tex

@@ -1,3 +1,5 @@
+% ******************************* Thesis Appendix A ********************************
+
 \chapter{Appendix A}
 
 and here I put a bit of postamble ...

Appendix2/appendix2.tex

@@ -1,3 +1,5 @@
+% ******************************* Thesis Appendix B ********************************
+
 \chapter{Appendix B}
 
 and here I put some more postamble ...

Classes/PhDThesisPSnPDF.cls

@@ -100,26 +100,36 @@
   \PassOptionsToClass{\CurrentOption}{book}
 }
 
-
+% Determine whether to run pdftex or dvips
 \ProcessOptions\relax%
-
-\ifx\pdfoutput\undefined%
-      \LoadClass[dvips,fleqn,openright]{book}%
-      \@ifundefined{pdfoutput}{
-        \AtBeginDvi{\special{papersize=\paperwidth,\paperheight}}
-      }
-
-\else%
-      \LoadClass[pdftex,fleqn,openright]{book}%
-      \AtBeginDvi{\special{papersize=\paperwidth,\paperheight}}%
-\fi%
-
+\newif\ifsetDVI\setDVIfalse
+\ifx\pdfoutput\undefined
+  % we are not running PDFLaTeX
+  \LoadClass[dvips,fleqn,openright]{book}%
+  \AtBeginDvi{\special{papersize=\paperwidth,\paperheight}}
+  \setDVItrue
+\else % we are running PDFLaTeX
+  \ifnum \pdfoutput>0
+    %PDF-Output
+    \setDVIfalse
+    \LoadClass[pdftex,fleqn,openright]{book}%
+  \else
+    %DVI-output
+    \setDVItrue
+    \LoadClass[fleqn,openright]{book}%
+    \AtBeginDvi{\special{papersize=\paperwidth,\paperheight}}
+  \fi
+\fi
 
 % **************************** Print / Online ***************************
 % Defines a print / online version to define page-layout and hyperrefering 
 
 \if@print
+        \ifsetDVI
+	\RequirePackage[dvips]{hyperref}
+        \else
 	\RequirePackage{hyperref}
+        \fi
 	% For Print version
 	\hypersetup{
           plainpages=false, 
@@ -150,7 +160,12 @@
     	\hypersetup{pdfpagelayout=OneColumn}
         \fi
 \else
+        \ifsetDVI
+	\RequirePackage[dvips]{hyperref}
+        \else
 	\RequirePackage{hyperref}
+        \fi
+
 	% For PDF Online version
 	\hypersetup{
           plainpages=false,
@@ -204,10 +219,10 @@
 
 % **************************** Graphics and Figures ****************************
 \RequirePackage[usenames, dvipsnames]{color} 
-% Convert eps figures to pdf
-\RequirePackage{epstopdf} 
 \ifpdf 
-	\RequirePackage[pdftex]{graphicx}
+        % Convert eps figures to pdf
+        \RequirePackage{epstopdf} 
+        \RequirePackage[pdftex]{graphicx}
 	\DeclareGraphicsExtensions{.png, .jpg, .pdf}
 	\pdfcompresslevel=9
 	\graphicspath{{Figs/Raster/}{Figs/}}

Declaration/declaration.tex

@@ -1,14 +1,9 @@
-% Thesis Declaration ---------------------------------------------------
+% ******************************* Thesis Declaration ********************************
 
-\begin{declaration} %this creates the heading for the dedication page
+\begin{declaration}
 
 I hereby declare that except where specific reference is made to the work of others, the contents of this dissertation are original and have not been submitted in whole or in part for consideration for any other degree or qualification in this, or any other University. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration, except where specifically indicated in the text. This dissertation contains less than 65,000 words including appendices, bibliography, footnotes, tables and equations and has less than 150 figures.
 
-% If you have obtained permission!
-
-%Permission has been granted by board of graduate studies to exceed the recommended limits 150 figures and to include a CD-ROM in the dissertation. This dissertation is presented less than 65,000 words and 210 figures.
-
-
 % Author and date will be inserted automatically from thesis.tex \author \degreedate
 
 \end{declaration}

Dedication/dedication.tex

@@ -1,14 +1,8 @@
-% Thesis Dedictation ---------------------------------------------------
+% ******************************* Thesis Dedidcation ********************************
 
-\begin{dedication} %this creates the heading for the dedication page
+\begin{dedication} 
 
 I would like to dedicate this thesis to my loving parents ...
 
 \end{dedication}
 
-% ----------------------------------------------------------------------
-
-%%% Local Variables: 
-%%% mode: latex
-%%% TeX-master: "../thesis"
-%%% End: 

thesis.tex

@@ -1,7 +1,7 @@
 % ******************************* PhD Thesis Template ************************
 % Please have a look at the README.md file for info on how to use the template
 
-\documentclass[times,twoside,numbered,print,index]{Classes/PhDThesisPSnPDF}
+\documentclass[times,twoside,numbered,index]{Classes/PhDThesisPSnPDF}
 
 % *****************************************************************************
 % ******************************* Class Options *******************************