Polishing of the main part of the msc template

HY-CS-main.tex

@@ -96,8 +96,7 @@
 
 
 % Set supervisors, use the titles according to the thesis language
-% Prof. 
-% Dr. or in Finnish toht. or tri or FT, TkT, Ph.D. or in Swedish... 
+% in English Prof. or Dr., or in Finnish toht. or tri or FT, TkT, Ph.D. or in Swedish... 
 \supervisors{Prof.~D.U.~Mind, Dr.~O.~Why}
 
 
@@ -182,11 +181,7 @@ Finally, specify 1--3 ACM Computing Classification System (CCS) topics, as per \
 Each topic is specified with one path, as shown in the example below, and elements of the path separated with an arrow.
 Emphasis of each element individually can be indicated
 by the use of bold face for high importance or italics for intermediate
-level. 
-
-If you are writing your thesis in Latex, then examine the Latex file for commands that allow you to easily specify various elements of the thesis (e.g., its title or the names of the supervisors).
-
-If you are writing your thesis in Microsoft Word or similar software, then edit the various elements of the template directly.
+level.
 
 \end{abstract}
 \end{otherlanguage}
@@ -223,16 +218,21 @@ If you are writing your thesis in Microsoft Word or similar software, then edit
 \backmatter
 \begin{appendices}
 
-%\input{instructions_english}
-\input{instructions_finnish}
+\appendix{Sample Appendix\label{appendix:sample}}
+
+You can add an appendix to your thesis.
 
-\appendix{Sample Appendix\label{appendix:model}}
-usually starts on its own page, with the name and number of the appendix at the top. 
-The appendices here are just models of the table of contents and the presentation. Each appendix
+An appendix starts on its own page, with the name and number of the appendix at the top. 
 Each appendix is paginated separately.
 
-In addition to complementing the main document, each appendix is also its own, independent entity.
-This means that an appendix cannot be just an image or a piece of programming, but the appendix must explain its contents and meaning.
+\appendix{Another Appendix\label{appendix:another}}
+
+You can have more than one appendices.
+
+%% another appendix
+\input{instructions_english}
+%% yet another appendix
+% \input{instructions_finnish}
 
 \end{appendices}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

instructions_english.tex

 
-\appendix{Template instructions}
+\appendix{Instructions for LaTex}
 
+\section{General Setup}
 
 In the HY-CS-main.tex file you will find the following STEPS 0--5. Bellow instructions what each STEP means and how to set up your thesis by following these STEPS.
 \vspace{0.5cm}
@@ -55,3 +56,49 @@ Your abstract text goes here.
 \begin{itemize}
 \item The default is Numbering alphabetic order, which should be used in most cases.
 \end{itemize}
+
+\section{Bibliography in Latex}
+
+The bibliography is defined in a separate .bib-file. For this template, it is named \texttt{bibliography.bib} and includes the following content:
+\begin{verbatim}
+@article{einstein,
+    author =       "Albert Einstein",
+    title =        "{Zur Elektrodynamik bewegter K{\"o}rper}. ({German})
+        [{On} the electrodynamics of moving bodies]",
+    journal =      "Annalen der Physik",
+    volume =       "322",
+    number =       "10",
+    pages =        "891--921",
+    year =         "1905",
+    DOI =          "http://dx.doi.org/10.1002/andp.19053221004"
+}
+ 
+@book{latexcompanion,
+    author    = "Michel Goossens and Frank Mittelbach and Alexander Samarin",
+    title     = "The \LaTeX\ Companion",
+    year      = "1993",
+    publisher = "Addison-Wesley",
+    address   = "Reading, Massachusetts"
+}
+ 
+@misc{knuthwebsite,
+    author    = "Donald Knuth",
+    title     = "Knuth: Computers and Typesetting",
+    url       = "http://www-cs-faculty.stanford.edu/%7Eknuth/abcde.html"
+}
+\end{verbatim}
+
+In the last reference url field the code \verb+%7E+ will translate into \verb+~+ once clicked in the final pdf.
+
+References are created using command \texttt{\textbackslash cite\{einstein\}}, showing as \citep{einstein}. Other examples: \citep{latexcompanion,knuthwebsite}.
+
+For the style of bibliography and citations, see some options in \url{https://www.overleaf.com/learn/latex/Bibtex_bibliography_styles}.
+
+
+\section{Producing the thesis pdf}
+
+This template has been prepared in LaTeX for usage with Overleaf. If your LaTeX source files contain no errors, then Overleaf produces the pdf file automatically.
+
+Of course, you are allowed to use the LaTeX template in other systems, but make sure you know how to produce the pdf file there. 
+For example, in Linux, you typically need to execute the commands \texttt{pdflatex mainfile.tex} and \texttt{biber mainfile.tex} repeatedly until no more warnings are shown. This process can be automised using make-command. 
+Note that normally we would be using \texttt{bibtex} command instead of \texttt{biber} but because of the biblatex package \texttt{biber} should be used.

msc_english_contents.tex

 \chapter{Introduction}
 
-The following gives some superficial instructions for using this template for a Master's thesis. For guidelines on thesis writing you can consult various sources, for example, university courses on scientific writing or your supervisors.
+The following gives some superficial instructions for using this template for a Master's thesis. For guidelines on thesis writing you can consult various sources, such as university courses on scientific writing or your supervisors.
 
-The thesis should have an introduction chapter. Other chapters can be named according to the topic. In the end, some summary chapter is needed; see Chapter~\ref{chapter:conclusions} for an example.
+The thesis should have an introduction chapter. Other chapters can be named according to the topic. In the end, a concluding chapter is needed; see Chapter~\ref{chapter:conclusions} for an example.
 
 \chapter{Figures and Tables}
 
@@ -43,53 +43,22 @@ $A+B$ & 10.5 & 1.0 & 1.6 \\
 \end{center}
 \end{table}
 
-\chapter{Citations}
-
-\section{Citations to literature}
-
-References are listed in a separate .bib-file. In this case it is named \texttt{bibliography.bib} including the following content:
-\begin{verbatim}
-@article{einstein,
-    author =       "Albert Einstein",
-    title =        "{Zur Elektrodynamik bewegter K{\"o}rper}. ({German})
-        [{On} the electrodynamics of moving bodies]",
-    journal =      "Annalen der Physik",
-    volume =       "322",
-    number =       "10",
-    pages =        "891--921",
-    year =         "1905",
-    DOI =          "http://dx.doi.org/10.1002/andp.19053221004"
-}
- 
-@book{latexcompanion,
-    author    = "Michel Goossens and Frank Mittelbach and Alexander Samarin",
-    title     = "The \LaTeX\ Companion",
-    year      = "1993",
-    publisher = "Addison-Wesley",
-    address   = "Reading, Massachusetts"
-}
- 
-@misc{knuthwebsite,
-    author    = "Donald Knuth",
-    title     = "Knuth: Computers and Typesetting",
-    url       = "http://www-cs-faculty.stanford.edu/%7Eknuth/abcde.html"
-}
-\end{verbatim}
-
-In the last reference url field the code \verb+%7E+ will translate into \verb+~+ once clicked in the final pdf.
-
-References are created using command \texttt{\textbackslash cite\{einstein\}}, showing as \citep{einstein}. Other examples: \citep{latexcompanion,knuthwebsite}.
-
-Citation style can be negotiated with the supervisor. See some options in \url{https://www.sharelatex.com/learn/Bibtex_bibliography_styles}.
+\chapter{References}
 
-\section{Crossreferences}
-
-Appendix~\ref{appendix:model} on page~\pageref{appendix:model} contains some additional material.
+It is very likely that, at various points in your thesis, you will need refer to other parts of the thesis or even to other works from the literature.
+%
+Referring to other parts of the thesis is usually straightforward --- e.g., ``see
+Appendix~\ref{appendix:sample} for some additional material'' or ``see Figure~\ref{fig:logo} on page~\pageref{fig:logo}''.
 
-\chapter{From tex to pdf}
+To refer to other works in the literature, make sure you include a ``Bibliography'' chapter after the concluding chapter that lists all the works that you refer to in your text; and that you refer to the works in the bibliography using an appropriate \emph{citation key}.
+%
+This thesis template contains an example of a bibliography.
+%
+As an example of a citation key, we can write \citep{einstein} to refer to the work written by Einstein in 1905, as it appears in the bilbliography included in this template.
 
-In Linux, run \texttt{pdflatex filename.tex} and \texttt{biber filename.tex} repeatedly until no more warnings are shown. This process can be automised using make-command.
-Note that normally we would be using \texttt{bibtex} command instead of \texttt{biber} but because of the biblatex package \texttt{biber} should be used.
+Note that there are different possible styles for the bibliography and citation keys.
+%
+You may consult your supervisors on the chosen style -- and once you arrive at a preferred style, use it consistently throughout the thesis.
  
 \chapter{Conclusions\label{chapter:conclusions}}