diff --git a/LuaUUThesis.cls b/LuaUUThesis.cls
index f077a9c..1b2d09f 100644
--- a/LuaUUThesis.cls
+++ b/LuaUUThesis.cls
@@ -1,16 +1,213 @@
+% ==============================================
+%   Class definition UU LuaThesis - 2018-01-18
+% ==============================================
+
 \ProvidesClass{LuaUUThesis}
 \NeedsTeXFormat{LaTeX2e}
 
+% Conditionals for options
+\newif\if@UU@chapterafterpart
+\newif\if@usepdfgfx
+\newif\if@sfivepaper
+\newif\if@culumntitles
+\newif\if@UU@openright
+\newif\if@UU@margnum
+
+\@usepdfgfxtrue
+\@sfivepapertrue
+\@UU@chapterafterparttrue
+\@culumntitlesfalse
+\@UU@openrightfalse
+
+% Paper resizing commands
+\providecommand{\UU@setsfivepaper}{
+	\setlength{\paperheight}{242mm}
+	\setlength{\paperwidth}{165mm}
+	\setlength{\hoffset}{-1in}
+	\setlength{\voffset}{-1in}
+	\setlength{\topmargin}{8,8mm}
+	\setlength{\oddsidemargin}{22,5mm}
+	\setlength{\evensidemargin}{22,5mm}
+	\setlength{\headheight}{4,6mm}
+	\setlength{\headsep}{4,6mm}
+	\setlength{\textheight}{572pt}
+	\setlength{\textwidth}{120mm}
+	\setlength{\marginparsep}{1mm}
+	\setlength{\marginparwidth}{20mm}
+	\setlength{\footskip}{26pt}
+	\setlength{\topskip}{13pt}
+	\setlength{\pdfpagewidth}{\paperwidth}
+	\setlength{\pdfpageheight}{\paperheight}
+}
+
+% extra-large margins for use during draft
+% Note that this is effectively s5paper format
+% with all extra space used for margins (out to a4paper dimensions)
+\providecommand{\UU@setafourpaper}{
+	\setlength{\paperheight}{297mm} %242mm % 55mm
+	\setlength{\paperwidth}{210mm}  %165mm % 45mm
+	\setlength{\hoffset}{-1in}
+	\setlength{\voffset}{-1in}
+	% add half the excess height to topmargin (plus original value)
+	\setlength{\topmargin}{36,3mm} % 8.8 + 0.5 * 55
+	% add 50 percent of the excess width to oddsidemargin (plus original value)
+	\setlength{\oddsidemargin}{45mm} % 22.5 + 0.50 * 45
+	\setlength{\evensidemargin}{45mm}
+	\setlength{\headheight}{4,6mm}
+	\setlength{\headsep}{4,6mm}
+	% keep textheight and textwidth same as for s5paper
+	% remember, the idea here was to expand the margins, to make room
+	% for more marginnotes during draft work
+	\setlength{\textheight}{572pt}
+	\setlength{\textwidth}{120mm}
+	\setlength{\marginparsep}{1mm}
+	% add 50 percent of the excess page width to marginparwidth (plus original value)
+	% remember, marginparwidth should be slightly smaller than odd/evensidemargin
+	\setlength{\marginparwidth}{42,5mm} % 20 + 0.50 * 45
+	\setlength{\footskip}{26pt}
+	\setlength{\topskip}{13pt}
+	\setlength{\pdfpagewidth}{\paperwidth}
+	\setlength{\pdfpageheight}{\paperheight}
+	\special{papersize=297mm,210mm}
+}
+\providecommand{\UU@setafivepaper}{
+	\setlength{\paperheight}{210mm}
+	\setlength{\paperwidth}{148mm}
+	\setlength{\hoffset}{-1in}
+	\setlength{\voffset}{-1in}
+	\setlength{\topmargin}{8,8mm}
+	\setlength{\oddsidemargin}{20mm}
+	\setlength{\evensidemargin}{20mm}
+	\setlength{\headheight}{4,6mm}
+	\setlength{\headsep}{4,6mm}
+	\setlength{\textheight}{172mm}
+	\setlength{\textwidth}{108mm}
+	\setlength{\marginparsep}{1mm}
+	\setlength{\marginparwidth}{20mm}
+	\setlength{\footskip}{26pt}
+	\setlength{\pdfpagewidth}{\paperwidth}
+	\setlength{\pdfpageheight}{\paperheight}
+}
+\providecommand{\UU@setbfivepaper}{
+	\setlength{\paperheight}{250mm}
+	\setlength{\paperwidth}{176mm}
+	\setlength{\hoffset}{-1in}
+	\setlength{\voffset}{-1in}
+	\setlength{\topmargin}{8,8mm}
+	\setlength{\oddsidemargin}{22,5mm}
+	\setlength{\evensidemargin}{22,5mm}
+	\setlength{\headheight}{4,6mm}
+	\setlength{\headsep}{4,6mm}
+	\setlength{\textheight}{210mm}
+	\setlength{\textwidth}{131mm}
+	\setlength{\marginparsep}{1mm}
+	\setlength{\marginparwidth}{20mm}
+	\setlength{\footskip}{26pt}
+	\setlength{\pdfpagewidth}{\paperwidth}
+	\setlength{\pdfpageheight}{\paperheight}
+}
+
+\providecommand{\UU@papersize}{}
+\let\UU@papersize\UU@setsfivepaper
+
+
+\DeclareOption{s5paper}{
+	\let\UU@papersize\UU@setsfivepaper
+}
+
+\DeclareOption{a4paper}{
+	\PassOptionsToClass{\CurrentOption}{book}
+	\PassOptionsToPackage{\CurrentOption}{geometry}
+	\PassOptionsToPackage{\CurrentOption}{hyperref}
+	\let\UU@papersize\UU@setafourpaper
+}
+\DeclareOption{a5paper}{
+	\PassOptionsToClass{\CurrentOption}{book}
+	\PassOptionsToPackage{\CurrentOption}{geometry}
+	\PassOptionsToPackage{\CurrentOption}{hyperref}
+	\@sfivepaperfalse
+	\let\UU@papersize\UU@setafivepaper
+}
+\DeclareOption{b5paper}{
+	\PassOptionsToClass{\CurrentOption}{book}
+	\PassOptionsToPackage{\CurrentOption}{geometry}
+	\PassOptionsToPackage{\CurrentOption}{hyperref}
+	\let\UU@papersize\UU@setbfivepaper
+}
+\DeclareOption{letterpaper}{
+	\ClassWarning{Invalid papersize \CurrentOption}
+}
+\DeclareOption{legalpaper}{
+	\ClassWarning{Invalid papersize \CurrentOption}
+}
+\DeclareOption{titles}{
+	\@culumntitlestrue
+}
+\DeclareOption{margnum}{
+	\@UU@margnumtrue
+}
+\DeclareOption{twocolumn}{
+	\ClassWarning{This class does not support \CurrentOption}
+}
+\DeclareOption{swedish}{ \PassOptionsToPackage{\CurrentOption}{babel} }
+\DeclareOption{english}{ \PassOptionsToPackage{\CurrentOption}{babel} }
+\DeclareOption{german}{ \PassOptionsToPackage{\CurrentOption}{babel} }
+\DeclareOption{french}{ \PassOptionsToPackage{\CurrentOption}{babel} }
+\DeclareOption{openany}{ \@UU@openrightfalse }
+\DeclareOption{openright}{ \@UU@openrighttrue }
+
+\PassOptionsToPackage{figuresright}{rotating}
+\PassOptionsToPackage{font=small,labelfont=bf,nooneline,textfont=it}{caption}
+\PassOptionsToPackage{linktocpage, breaklinks=true, colorlinks=true, urlcolor=black, linkcolor=black, citecolor=black, filecolor=black, menucolor=black, pdfpagelabels,bookmarksnumbered=true,bookmarks=true}{hyperref}
+
+\ProcessOptions
+
 % The thesis template is based on the standard class book
 \LoadClass{book}
+\if@UU@openright\@openrighttrue\else\@openrightfalse\fi
+
+\@ifpackageloaded{ifpdf}{%
+	\usepackage{ifpdf}%
+	\ifpdf%
+		\@usepdfgfxtrue%
+	\else%
+		\@usepdfgfxfalse%
+	\fi%
+}%
+
+%% disable this block since it seems to only be for dvips route anyway
+% Define page size and tell dvips to use it by entering the \special command
+%\UU@papersize
+%\special{papersize=\the\pdfpagewidth,\the\pdfpageheight}
+
+
+% ============================================
+%               Font settings
+% ============================================
+
+\AtBeginDocument{%
+	\renewcommand\normalsize{\@setfontsize{\normalsize}{11}{13}} %11/13pt
+	\renewcommand\small{\@setfontsize{\small}{10}{12}}%10/12pt
+	\renewcommand\footnotesize{\@setfontsize{\footnotesize}{9}{11}}%9/11pt
+	\renewcommand\scriptsize{\@setfontsize{\scriptsize}{8}{10}}%8/10pt
+	\renewcommand\tiny{\@setfontsize{\tiny}{6}{8}}%6/8pt
+	\renewcommand\large{\@setfontsize{\large}{13}{15}}%13/15
+	\renewcommand\Large{\@setfontsize{\Large}{15}{17}}%15/17
+	\renewcommand\LARGE{\@setfontsize{\LARGE}{18}{20}}%18/20
+	\renewcommand\huge{\@setfontsize{\huge}{20}{23}}%20/23
+	\renewcommand\Huge{\@setfontsize{\Huge}{24}{28}}%24/28
+
+	\let\superscript\textsuperscript
+	\let\subscript\textsubscript
+	\normalsize
+}
 
 
 % ============================================
 %                Basic adjustments
 % ============================================
 
-% disabled for now /TA
-% \renewcommand{\bibname}{\refname}
+\renewcommand{\bibname}{\refname}
 
 % Prevent widows and orphans by setting a very large penalty
 \widowpenalty=\@M
@@ -93,6 +290,68 @@
 	\advance\linewidth-\@totalleftmargin
 }
 
+% Indented, smaller text with space before and after
+% (You should adjust this so it uses csquotes quotation environment /TA, 180118)
+\renewenvironment{quotation}{%
+	\par\addtolength{\leftskip}{26pt}%
+	\addvspace{13pt plus 6pt minus 6pt}\small\noindent\ignorespaces%
+}{%
+	\par\addvspace{13pt plus 6pt minus 6pt}%
+	\global\@afterindentfalse\ignorespacesafterend%
+}
+\let\quote\quotation
+\let\endquote\endquotation
+
+
+% ============================================
+%             Page layout
+% ============================================
+
+% Plain - Empty header with page number outer end of footer
+\renewcommand{\ps@plain}{%
+	\let\@oddhead\@empty%
+	\let\@evenhead\@empty%
+	\renewcommand{\@oddfoot}{\hfil\thepage}%
+	\renewcommand{\@evenfoot}{\thepage\hfil}%
+}
+
+% UU@chapter - empty header
+\providecommand{\ps@UU@chapter}{%
+	\let\@oddhead\@empty%
+	\let\@evenhead\@empty%
+}
+
+% Headings - chapter title in even headers, section title in odd headers
+\renewcommand{\ps@headings}{%
+	\ps@plain%
+	\def\@evenhead{\leftmark\hfil }%
+	\def\@oddhead {\hfil\rightmark }%
+	\let\@mkboth \markboth %
+	\def\chaptermark ##1{\markboth {\ifnum \c@secnumdepth >\m@ne \thechapter . \ \fi ##1}{}}%
+	\def\sectionmark ##1{\markright {\ifnum \c@secnumdepth >\z@ \thesection~~\fi ##1}}%
+}
+
+\let\@oddfoot\@empty
+\let\@evenfoot\@empty
+\let\@mkboth\@gobbletwo
+\let\chaptermark\@gobble
+\let\sectionmark\@gobble
+\def\appendixmark#1{%
+	\markboth{Appendix \theappendix}{}%
+}
+
+\AtBeginDocument{
+	\pagestyle{plain}
+}
+
+% Adjust to odd pagenumber using an optional blank page
+\let\origdoublepage\cleardoublepage
+\newcommand{\clearemptydoublepage}{%
+  \clearpage
+  {\pagestyle{empty}\origdoublepage}%
+}
+\let\cleardoublepage\clearemptydoublepage
+
 
 % ============================================
 %          Dispositional Settings
@@ -105,6 +364,57 @@
 \newcounter{secnumdepthmainmatter}
 \AtBeginDocument{\setcounter{secnumdepthmainmatter}{\c@secnumdepth}}
 
+% Remove page numbers and numbering of headings
+\let\oldfrontmatter\frontmatter
+\renewcommand{\frontmatter}{%
+	\renewcommand{\thepage}{\roman{page}}%
+	\setcounter{secnumdepth}{-2} %
+	\@mainmatterfalse%
+	\pagestyle{empty}%
+}
+
+% Adjust to odd page and restore numbering of headings
+\let\oldmainmatter\mainmatter
+	\renewcommand{\mainmatter}{%
+	\cleardoublepage%
+	\renewcommand{\thepage}{\arabic{page}}%
+	\setcounter{secnumdepth}{\c@secnumdepthmainmatter} %
+	\@mainmattertrue%
+	\if@culumntitles%
+		\pagestyle{headings}%
+	\else%
+		\pagestyle{plain}%
+	\fi%
+}
+
+% Remove page numbers and numbering of headings
+\let\oldbackmatter\backmatter
+\renewcommand{\backmatter}{%
+	\oldbackmatter%
+	\setcounter{secnumdepth}{-2}
+	\makeatletter%
+	\ifx\toclevel@chapter\undefined\else%
+		\renewcommand{\toclevel@appendix}{-1}%
+		\renewcommand{\toclevel@chapter}{-1}%
+		\renewcommand{\toclevel@section}{0}%
+		\renewcommand{\toclevel@subsection}{1}%
+		\renewcommand{\toclevel@subsubsection}{2}%
+		\renewcommand{\toclevel@paragraph}{3}%
+		\renewcommand{\toclevel@subparagraph}{4}%
+	\fi%
+	\makeatother%
+}
+
+% Change the chapter command to create appendixes
+\renewenvironment{appendix}{
+	\@ifundefined{pdfbookmark}{}{\pdfbookmark[-2]{\appendixname}{appendices}}%
+	\let\oldchapter\chapter%
+	\let\chapter\appendixchapter%
+	\let\chaptername\appendixname%
+	\@mainmattertrue%
+}{%
+}
+
 
 % ============================================
 %                  Headings
@@ -124,19 +434,337 @@
    \setcounter{secnumdepth}{\csname toclevel@#1\endcsname}%
 }
 
+% Redefinition of sectioning command to prevent issues with AMSMath
+% and allow for greater adjustments of chapter numbering
+
+\newcommand\chapterfont{}
+\let\uu@ifstar\@ifstar
+\renewcommand{\@startsection}[6]{ %
+	\if@noskipsec\leavevmode\fi %
+	\par\@tempskipa #4\relax\@afterindentfalse%
+	\if@nobreak%
+		\everypar{}%
+	\else%
+		\addpenalty\@secpenalty\addvspace\@tempskipa%
+	\fi%
+	\uu@ifstar{%
+		\@ssect{#3}{#4}{#5}{#6}%
+	}{%
+		\@dblarg{\@sect{#1}{#2}{#3}{#4}{#5}{#6}}%
+	}%
+}
+\def\@ssect#1#2#3#4#5{%
+	\@tempskipa #3\relax %
+	\begingroup %
+		#4{\@hangfrom{\hskip #1}\interlinepenalty \@M #5\@@par}%
+	\endgroup %
+	\@xsect{#3}%
+}
+\def\@sect#1#2#3#4#5#6[#7]#8{
+	\ifnum #2>\c@secnumdepth%
+		%\phantomsection%
+		\let\@svsec\@empty%
+	\else %
+		\refstepcounter{#1}%
+		\protected@edef\@svsec{\protect\@seccntformat{#1}\relax}%
+	\fi %
+	\@tempskipa #5\relax %
+	\begingroup %
+		#6%
+		{\@hangfrom {\hskip #3\relax \@svsec }\interlinepenalty \@M #8 \@@par }%
+	\endgroup%
+	\csname #1mark\endcsname {#7}%
+	\addcontentsline {toc}{#1}{%
+		\ifnum #2>\c@secnumdepth\else%
+			\protect\numberline{\csname the#1\endcsname}%
+		\fi%
+		#7%
+		}%
+	\@xsect{#5}
+}
+\def\@xsect#1{%
+	\@tempskipa #1\relax %
+		\par \nobreak \vskip \@tempskipa %
+		\@afterheading %
+	\ignorespaces%
+}
+
+% Chapter numbering formats
+\newcommand{\@seccntformat@part}{%
+	{\partname~\thepart}\hspace{0,5em}%
+}
+\newcommand{\@seccntformat@chapter}{%
+	{\thechapter}.\hspace{0,5em}%
+}
+\newcommand{\@seccntformat@section}{%
+	{\thesection}\hspace{0,5em}%
+}
+\newcommand{\@seccntformat@subsection}{{\thesubsection}\hspace{0,5em}}
+\newcommand{\@seccntformat@subsubsection}{{\thesubsubsection}\hspace{0,5em}}
+\newcommand{\@seccntformat@paragraph}{{\theparagraph}\hspace{0,5em}}
+\newcommand{\@seccntformat@subparagraph}{{\thesubparagraph}\hspace{0,5em}}
+\renewcommand{\@seccntformat}[1]{%
+		\csname @seccntformat@#1\endcsname%
+}
+
+\if@UU@margnum
+	\renewcommand{\@seccntformat}[1]{%
+		\makebox[0mm][r]{\csname @seccntformat@#1\endcsname}%
+	}
+\fi
+
+% Part heading
+\renewcommand{\part}{%
+	\cleardoublepage%
+	\thispagestyle {empty}%
+	\@afterindentfalse%
+	\@UU@chapterafterparttrue%
+	\secdef\@part\@spart%
+}
+\renewcommand{\@part}[2][1]{%
+	\edef\@mtarg{\zap@space#2 \@empty}%
+	\vspace*{0.3\textheight}%
+	\edef\pgsdelimiter{\ifx\@empty\@mtarg\else :\fi}%
+	\ifnum \c@secnumdepth >-2\relax %
+		\refstepcounter{part}%
+		\addcontentsline{toc}{part}{\partname~\thepart :~#1}%
+	\else %
+		\addcontentsline {toc}{part}{#1}%
+	\fi %
+	\markboth{}{}%
+	{
+		\UU@RaggedRight%
+		\interlinepenalty \@M%
+		\chapterfont%
+		\LARGE%
+		\ifnum \c@secnumdepth >-2\relax \partname \nobreakspace \thepart\pgsdelimiter \par \fi %
+		#2\par%
+	}%
+	\@xsect{\baselineskip}
+}
+
+% Chapter heading
+\renewcommand\chapter{%
+	\if@openright\cleardoublepage\else\if@UU@chapterafterpart\cleardoublepage\else\clearpage\fi\fi
+	\@UU@chapterafterpartfalse
+	%\markboth{}{}
+	\thispagestyle{UU@chapter}
+	\suppressfloats[t]
+	\@startsection {chapter}{0}{\z@}{\z@}{82pt plus 13pt minus 26pt}{%
+		\chapterfont%
+		\LARGE%
+		\UU@RaggedRight%
+		\hyphenpenalty=10000%
+	}%
+}
+\renewcommand\@makeschapterhead[1]{\chapter*{#1}}
+
+% Appendix heading
+\newcounter{appendix}
+\def\theappendix{\@Alph\c@appendix}%
+\def\appendixchapter{%
+	\if@openright\cleardoublepage\else\if@UU@chapterafterpart\cleardoublepage\else\clearpage\fi\fi
+	\@UU@chapterafterpartfalse
+	\thispagestyle{UU@chapter}
+	\suppressfloats[t]
+	\@startsection{appendix}{-2}{\z@}{\z@}{82pt plus 13pt minus 26pt}{%
+		\chapterfont%
+		\LARGE%
+		\UU@RaggedRight
+		Appendix \@Alph\c@appendix.\\
+	}%
+}
+
+\renewcommand\section{%
+	\@startsection {section}{1}{\z@}{30pt plus 5pt minus 5pt}{5pt minus 1pt}{%
+		\chapterfont%
+		\Large%
+		\UU@RaggedRight%
+		\hyphenpenalty=10000%
+	}%
+}
+\renewcommand\subsection{%
+	\@startsection {subsection}{2}{\z@}{25pt plus 5pt minus 3pt}{4pt minus 1pt}{%
+		\chapterfont%
+		\large%
+		\UU@RaggedRight%
+		\hyphenpenalty=10000%
+	}%
+}
+\renewcommand\subsubsection{%
+	\@startsection {subsubsection}{3}{\z@}{13pt plus 5pt minus 2pt}{1pt minus 1pt}{%
+		\chapterfont%
+		\normalsize%
+		\UU@RaggedRight%
+		\hyphenpenalty=10000%
+		\textbf
+	}%
+}
+\renewcommand\paragraph{%
+	\@startsection {paragraph}{4}{\z@}{13pt plus 5pt minus 2pt}{1pt minus 1pt}{%
+		\chapterfont%
+		\normalsize%
+		\UU@RaggedRight%
+		\hyphenpenalty=10000%
+		\textit
+	}%
+}
+\renewcommand\subparagraph{%
+	\@startsection {subparagraph}{5}{\z@}{13pt plus 5pt minus 2pt}{1pt minus 1pt}{%
+		\chapterfont%
+		\normalsize%
+		\UU@RaggedRight%
+		\hyphenpenalty=10000%
+	}%
+}
+
+%\hyphenation{te-star avsta-vning vi-d binde-streck}
+
+
+% ============================================
+%                 Captions
+% ============================================
+
+\setlength{\abovecaptionskip}{3pt plus 2pt}
+\setlength{\belowcaptionskip}{0pt plus 42pt}
+
+\AtBeginDocument{
+	\def\@caption#1[#2]#3{%
+		\par %
+		\addcontentsline {\csname ext@#1\endcsname }{#1}{\protect \numberline {\csname the#1\endcsname }{\ignorespaces #2}}%
+		\begingroup %
+			\@parboxrestore %
+			\if@minipage %
+				\@setminipage %
+			\fi %
+			\normalsize %
+			\@makecaption{\csname fnum@#1\endcsname }{\ignorespaces #3}%
+			\par %
+		\endgroup
+	}
+
+	\def\@makecaption@table#1#2{%
+		\addvspace{\belowcaptionskip}%
+		%\sbox\@tempboxa{{\bf #1.} #2}%
+		\small{\bf #1.} {\it #2}\par%
+		\addvspace{\abovecaptionskip}%
+	}
+
+	\def\@makecaption@default#1#2{%
+		\addvspace{\abovecaptionskip}%
+		\sbox\@tempboxa{{\it #1.} #2}%
+		\ifdim \wd\@tempboxa>\hsize%
+			\small{\it #1.} #2\par%
+		\else %
+			\global \@minipagefalse \hb@xt@ \hsize {\hfil \box \@tempboxa \hfil }%
+		\fi %
+		\addvspace{\belowcaptionskip}%
+	}
+
+	\renewcommand{\@makecaption}[2]{%
+		\expandafter\let\expandafter\hej\csname @makecaption@\@captype\endcsname%
+		\expandafter\ifx\hej\relax%
+			\let\hej\@makecaption@default%
+		\fi%
+		\hej{#1}{#2}%
+	}
+}
+
 
 % ============================================
 %              Package fixes
 % ============================================
 
+\AtBeginDocument{%
+%
+% Smaller font size in tables
+	\let\otable\table%
+	\def\table{\let\textnormalsize\normalsize\let\normalsize\small\par\otable}%
+	\g@addto@macro\endtable\normalsize%
+%
+% Fixes for package caption
+	\@ifpackageloaded{caption}{%
+		\let\captionfont\small%
+		\def\table{\begingroup\captionsetup{labelfont=bf}%
+		\small\par\otable}%
+		\g@addto@macro\endtable\endgroup%
+		\let\ofigure\figure%
+		\def \figure{\begingroup\captionsetup{labelfont=it,textfont=rm}\ofigure}%
+		\g@addto@macro\endfigure\endgroup%
+	}{}%
+%
+% Fixes for package natbib
+	\@ifpackageloaded{natbib}{%
+		\def\bibsection{\chapter{\bibname}\sectionmark{References}}%
+		\def\bibfont{\small}%
+		\def\bibpreamble{\UU@RaggedRight\raggedbottom}%
+	}{}%
+%
+% Fixes for package amsthm
+	\@ifpackageloaded{amsthm}{%
+		\def\th@definition{%
+		  \normalfont %
+		  \thm@preskip\baselineskip%
+		  \thm@postskip\thm@preskip%
+		}
+		\def\th@remark{%
+		  \thm@headfont{\itshape}%
+		  \normalfont %
+		  \thm@preskip\baselineskip%
+		  \thm@postskip\thm@preskip
+		}
+		\def\th@plain{%
+			\thm@preskip\baselineskip%
+			\thm@postskip\thm@preskip%
+			\itshape%
+		}%
+	}{}%
+%
+% Fixes for package longtable
+	\@ifpackageloaded{longtable}{%
+	\setlength\LTcapwidth{0.985\textwidth}%
+	\setlength\LTleft\z@%
+	\setlength\LTright\z@%
+		\def\LT@makecaption#1#2#3{%
+			\multicolumn{\LT@cols}{@{}l@{}}{%
+			\parbox{\LTcapwidth}{%
+			\def\@captype{table}%
+			\@makecaption{#2}{#3}}%
+			}%
+		}%
+		\let\olongtable\longtable%
+		\def\longtable{\small\par\olongtable}%
+		\g@addto@macro\endlongtable{\addvspace{0pt plus 13pt}\normalsize}%
+		\let\oLT@array\LT@array%
+	\def\LT@array[#1]#2{%
+	\oLT@array[#1]{#2}%
+	\hline \multicolumn{\LT@cols}{r@{}}{{\continuednextpage}} %
+	\endfoot}%
+	}{}%
+%
 % Prevents raggedright from creating bad line breaks
-\@ifpackageloaded{ragged2e}{
-	\providecommand{\UU@RaggedRight}{\RaggedRight}
-}{%
-	\providecommand{\UU@RaggedRight}{\raggedright\parfillskip\fill}%
+	\@ifpackageloaded{ragged2e}{
+		\providecommand{\UU@RaggedRight}{\RaggedRight}
+	}{%
+		\providecommand{\UU@RaggedRight}{\raggedright\parfillskip\fill}%
+	}
+%
+% Prevents hyperref from breaking table of contents
+	\@ifpackageloaded{hyperref}{
+		\def\toclevel@appendix{0}
+		\def\contentsline#1#2#3#4{%
+			\ifx \\#4\\\csname l@#1\endcsname {#2}{#3}%
+			\else %
+				\ifHy@linktocpage %
+					\csname l@#1\endcsname {#2}{\hyper@linkstart {link}{#4}{#3}\hyper@linkend }%
+				\else%
+					\csname l@#1\endcsname {\hyper@linkstart {link}{#4}{#2}\hyper@linkend }{#3}%
+				\fi%
+			\fi%
+		}
+	}{\providecommand{\phantomsection}{}}
 }
 
-
 % ============================================
 %             Table of contents
 % ============================================
@@ -146,13 +774,212 @@
    \setcounter{tocdepth}{\csname toclevel@#1\endcsname}%
 }
 
+\newlength{\tocskip@part}
+\setlength{\tocskip@part}{13pt plus 2pt}
+\newlength{\tocskip@chapter}
+\setlength{\tocskip@chapter}{8pt minus 1pt}
+\newlength{\@tempdimd}
+
+\newcommand\customtocline[5]{%
+	\ifnum \c@tocdepth >#5
+		\setlength\@tempdima{#4}%
+		\setlength\@tempdimb{#3}%
+		\settowidth{\@tempdimc}{~#2}%
+		\setlength{\@tempdimd}{\textwidth}%
+		\parindent \z@%
+		\begingroup%
+			\UU@RaggedRight%
+			\setlength{\parfillskip}{-\@tempdimc}%
+			%\advance\leftskip\@tempdima%
+			\advance\rightskip\@tempdimc%
+			\hskip -\leftskip%
+			\advance\leftskip\@tempdimb%
+			#1\nobreak\ %
+			{\tiny\dotfill}\nobreak{}\null%
+			~#2%
+		\par%
+		\endgroup%
+	\fi%
+}
+
+\renewcommand*{\numberline}[1]{\@hangfrom{\hb@xt@ \@tempdima {#1\hfil}}}
+\newcommand*\nonumberline[1]{\hb@xt@ \@tempdima {#1\hfil}}
+% List of tables TOC line: format of first part
+\newcommand*\tablenumberline[1]{\hb@xt@ \@tempdima {#1~\hfil}}
+% List of figures TOC line: format of first part
+\newcommand*\figurenumberline[1]{\hb@xt@ \@tempdima {#1~\hfil}}
+\newcommand*\partnumberline[1]{\partname~#1:~}
+\newcommand*\appendixnumberline[1]{\appendixname~#1:~}
+\let\chapternumberline\numberline
+%\newcommand*\chapternumberline[1]{}
+%{{\small\textsc\chaptername~#1\hfill\null\\\hskip-\leftskip}}
+\let\stdnumberline\numberline
+
+\newcommand{\settocnumwidth}[6]{
+	\settowidth{\tocnumindent@chapter}{#1\hspace{0.5em}}
+	\settowidth{\tocnumindent@section}{#1.#2\hspace{0.5em}}
+	\settowidth{\tocnumindent@subsection}{#1.#2.#3\hspace{0.5em}}
+	\settowidth{\tocnumindent@subsubsection}{#1.#2.#3.#4\hspace{0.5em}}
+	\settowidth{\tocnumindent@paragraph}{#1.#2.#3.#4.#5\hspace{0.5em}}
+	\settowidth{\tocnumindent@subparagraph}{#1.#2.#3.#4.#5.#6\hspace{0.5em}}
+	\adjusttocindent
+}
+\newcommand{\settocindent}[6]{
+	\setlength{\tocindent@chapter}{#1}
+	\setlength{\tocindent@section}{#2}
+	\setlength{\tocindent@subsection}{#3}
+	\setlength{\tocindent@subsubsection}{#4}
+	\setlength{\tocindent@paragraph}{#5}
+	\setlength{\tocindent@subparagraph}{#6}
+}
+\newcommand{\adjusttocindent}{
+	\setlength{\tocindent@section}{\tocindent@chapter}%
+	\ifnum\c@secnumdepthmainmatter>-1\addtolength{\tocindent@section}{\tocnumindent@chapter}%
+	\else\addtolength{\tocindent@section}{\tocindent}\fi%
+%
+	\setlength{\tocindent@subsection}{\tocindent@section}%
+	\ifnum\c@secnumdepthmainmatter>0\addtolength{\tocindent@subsection}{\tocnumindent@section}%
+	\else\addtolength{\tocindent@subsection}{\tocindent}\fi%
+%
+	\setlength{\tocindent@subsubsection}{\tocindent@subsection}%
+	\ifnum\c@secnumdepthmainmatter>1\addtolength{\tocindent@subsubsection}{\tocnumindent@subsection}%
+	\else\addtolength{\tocindent@subsubsection}{\tocindent}\fi%
+%
+	\setlength{\tocindent@paragraph}{\tocindent@subsubsection}%
+	\ifnum\c@secnumdepthmainmatter>2\addtolength{\tocindent@paragraph}{\tocnumindent@subsubsection}%
+	\else\addtolength{\tocindent@paragraph}{\tocindent}\fi%
+%
+	\setlength{\tocindent@subparagraph}{\tocindent@paragraph}%
+	\ifnum\c@secnumdepthmainmatter>3\addtolength{\tocindent@subparagraph}{\tocnumindent@paragraph}%
+	\else\addtolength{\tocindent@subparagraph}{\tocindent}\fi%
+}
+\newlength{\tocnumindent@chapter}
+\newlength{\tocnumindent@section}
+\newlength{\tocnumindent@subsection}
+\newlength{\tocnumindent@subsubsection}
+\newlength{\tocnumindent@paragraph}
+\newlength{\tocnumindent@subparagraph}
+\newlength{\tocindent}
+\newlength{\tocindent@chapter}
+\newlength{\tocindent@section}
+\newlength{\tocindent@subsection}
+\newlength{\tocindent@subsubsection}
+\newlength{\tocindent@paragraph}
+\newlength{\tocindent@subparagraph}
+
+\setlength{\tocindent}{13pt}
+%\settocnumindent{15pt}{24pt}{34pt}{44pt}{54pt}{64pt}
+%\settocnumwidth{10}{10}{5}{3}{3}{3}
+
+\setlength{\tocindent@chapter}{0pt}
+% Adjust table of contents indents based on level of numbering
+\AtBeginDocument{%
+	\settocnumwidth{10}{10}{5}{3}{3}{3}
+}
+
+\let\oldtableofcontents\tableofcontents
+\renewcommand{\tableofcontents}{%
+	\begingroup%
+		\raggedbottom%
+		\cleardoublepage%
+		\oldtableofcontents%
+		\vfill\null%
+		\clearpage%
+	\endgroup%
+}
+
+\newcounter{prevtoclvl}
+\setcounter{prevtoclvl}{-2}
+\newcommand{\@nopagebreaktoc}[1]{%
+	\ifnum\c@prevtoclvl<#1%
+		\nopagebreak[3]%
+	\fi%
+	\setcounter{prevtoclvl}{#1}%
+}
+
+\renewcommand*\l@chapter[2]{%
+	\@nopagebreaktoc{0}%
+	%\renewcommand{\numberline}{\chapternumberline}%
+	\vskip\tocskip@chapter%
+	\customtocline{#1}{#2}{\tocindent@chapter}{\tocnumindent@chapter}{-1}%
+	%\renewcommand{\numberline}{\stdnumberline}%
+}
+\renewcommand*\l@section[2]{\@nopagebreaktoc{1}\customtocline{#1}{#2}{\tocindent@section}{\tocnumindent@section}{0}}
+\renewcommand*\l@subsection[2]{\@nopagebreaktoc{2}\customtocline{#1}{#2}{\tocindent@subsection}{\tocnumindent@subsection}{1}}
+\renewcommand*\l@subsubsection[2]{\@nopagebreaktoc{4}\customtocline{#1}{#2}{\tocindent@subsubsection}{\tocnumindent@subsubsection}{2}}
+\renewcommand*\l@paragraph[2]{\@nopagebreaktoc{4}\customtocline{#1}{#2}{\tocindent@paragraph}{\tocnumindent@paragraph}{3}}
+\renewcommand*\l@subparagraph[2]{\nopagebreak[1]\@nopagebreaktoc{5}\customtocline{#1}{#2}{\tocindent@subparagraph}{\tocnumindent@subparagraph}{4}}
+\setcounter{tocdepth}{2}
+
+\newcommand*\l@appendix[2]{%
+	\@nopagebreaktoc{0}
+	\renewcommand{\numberline}{\appendixnumberline}%
+	\vskip\tocskip@chapter%
+	\customtocline{#1}{#2}{\tocindent@chapter}{\tocnumindent@chapter}{-1}%
+	\renewcommand{\numberline}{\stdnumberline}%
+}
+
+\renewcommand*\l@part[2]{%
+	\@nopagebreaktoc{-1}%
+	\renewcommand{\numberline}{\partnumberline}%
+	\vskip\tocskip@part%
+	\customtocline{#1}{#2}{\z@}{4em}{-2}%
+	\renewcommand{\numberline}{\stdnumberline}%
+}
+
+% Figure TOC number line
+\renewcommand*\l@figure[2]{%
+	\let\numberline\figurenumberline%
+	\customtocline{#1}{#2}{\z@}{2.2em}{0}%
+	\renewcommand{\numberline}{\stdnumberline}%
+}
+% Table TOC number line
+\renewcommand*\l@table[2]{%
+	\let\numberline\tablenumberline%
+	\customtocline{#1}{#2}{\z@}{2.2em}{0}%
+	\addvspace{0.5\baselineskip plus 0.1\baselineskip}%
+	\renewcommand{\numberline}{\stdnumberline}%
+}
+
+
+% ============================================
+%            Basic bibliography
+% ============================================
+
+\let\oldbib\thebibliography
+\let\endoldbib\endthebibliography
+
+\renewenvironment{thebibliography}[1]{%
+	\chapter{\bibname}%
+	\@mkboth {\bibname}{\bibname}%
+	\small%
+	\UU@RaggedRight%
+	\raggedbottom%
+	\list{\@biblabel{\@arabic\c@enumiv }}{%
+		\settowidth\labelwidth{\@biblabel{#1}}%
+		\leftmargin\labelwidth %
+		\advance\leftmargin \labelsep %
+		\@openbib@code%
+		\usecounter{enumiv}%
+		\let\p@enumiv\@empty %
+		\renewcommand\theenumiv{\@arabic \c@enumiv }%
+	}%
+	\sloppy %
+	\clubpenalty 4000 %
+	\@clubpenalty \clubpenalty %
+	\widowpenalty 4000%
+	\sfcode `\.\@m%
+}{%
+	\def \@noitemerr {\@latex@warning {Empty `thebibliography' environment}}%
+	\endlist%
+}
+
 
 % ============================================
 %                List of papers
 % ============================================
 
-% disabled for now /TA
-%\renewcommand{\bibname}{\refname}
+\renewcommand{\bibname}{\refname}
 \providecommand{\listofpapersname}{List of papers}
 \providecommand{\continuednextpage}{Continued on next page}
 \providecommand{\keywordsname}{Keywords}
@@ -338,6 +1165,43 @@
 }
 
 
+% ============================================
+%                    Index
+% ============================================
+
+\newcommand{\UU@theindex}{
+	\clearpage%
+	\if@twocolumn%
+		\@restonecolfalse %
+	\else %
+		\@restonecoltrue %
+	\fi %
+	\twocolumn%
+	\chapter{\indexname}%
+	\parindent\z@%
+	\parskip\z@ \@plus .3\p@ %
+	\relax %
+	\columnseprule \z@ %
+	\columnsep 35\p@ %
+	\let \item \@idxitem %
+}%
+
+\AtBeginDocument{%
+	\let\theindex\UU@theindex%
+	\@ifpackageloaded{makeidx}{%
+		\renewcommand{\printindex}{\@input {\jobname .ind}}%
+	}{}%
+	\@ifpackageloaded{multind}{%
+		\renewcommand{\printindex}[2]{%
+			{%
+			\def\indexname{#2}%
+			\@input{#1.ind}%
+			}%
+		}%
+	}{}%
+}
+
+
 % ============================================
 %        Compability and short-hands
 % ============================================