Clean up front matter formatting and TOC generation

thesis.lyx

@@ -242,6 +242,22 @@ End
 
 \begin_body
 
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Plain Layout
+
+
+\backslash
+pdfbookmark{Title page}{title}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
 \begin_layout Title
 Bioinformatic analysis of complex, high-throughput genomic and epigenomic
  data in the context of immunology and transplant rejection
@@ -292,6 +308,27 @@ in partial fulfillment of the requirements for the degree of
 October 2019
 \end_layout
 
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Plain Layout
+To remove TODOs and watermark: Add 
+\begin_inset Quotes eld
+\end_inset
+
+final
+\begin_inset Quotes erd
+\end_inset
+
+ to the document class custom options.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 \begin_inset ERT
 status open
@@ -319,19 +356,48 @@ Use roman numeral page numbers
 \end_layout
 
 \begin_layout Standard
-\begin_inset Note Note
-status open
+\begin_inset Newpage newpage
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset ERT
+status collapsed
 
 \begin_layout Plain Layout
-To remove TODOs and watermark: Add 
-\begin_inset Quotes eld
-\end_inset
 
-final
-\begin_inset Quotes erd
+
+\backslash
+phantomsection
+\end_layout
+
+\begin_layout Plain Layout
+
+
+\backslash
+addcontentsline{toc}{chapter}{Copyright notice}
+\end_layout
+
 \end_inset
 
- to the document class custom options.
+
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset ERT
+status collapsed
+
+\begin_layout Plain Layout
+
+
+\backslash
+vspace*{
+\backslash
+stretch{1}}
 \end_layout
 
 \end_inset
@@ -340,14 +406,28 @@ final
 \end_layout
 
 \begin_layout Standard
+\align center
+© 2019 by Ryan C.
+ Thompson
+\end_layout
+
+\begin_layout Standard
+\align center
+All rights reserved.
+\end_layout
+
+\begin_layout Standard
+\align center
 \begin_inset ERT
-status open
+status collapsed
 
 \begin_layout Plain Layout
 
 
 \backslash
-addcontentsline{toc}{chapter}{Copyright notice}
+vspace*{
+\backslash
+stretch{2}}
 \end_layout
 
 \end_inset
@@ -356,12 +436,23 @@ addcontentsline{toc}{chapter}{Copyright notice}
 \end_layout
 
 \begin_layout Standard
-[Copyright notice]
+\begin_inset Newpage newpage
+\end_inset
+
+
 \end_layout
 
 \begin_layout Standard
+\align center
 \begin_inset ERT
-status open
+status collapsed
+
+\begin_layout Plain Layout
+
+
+\backslash
+phantomsection
+\end_layout
 
 \begin_layout Plain Layout
 
@@ -376,12 +467,28 @@ addcontentsline{toc}{chapter}{Thesis acceptance form}
 \end_layout
 
 \begin_layout Standard
+\align center
 [Thesis acceptance form]
 \end_layout
 
 \begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align center
 \begin_inset ERT
-status open
+status collapsed
+
+\begin_layout Plain Layout
+
+
+\backslash
+phantomsection
+\end_layout
 
 \begin_layout Plain Layout
 
@@ -396,12 +503,66 @@ addcontentsline{toc}{chapter}{Dedication}
 \end_layout
 
 \begin_layout Standard
+\align center
+\begin_inset ERT
+status collapsed
+
+\begin_layout Plain Layout
+
+
+\backslash
+vspace*{
+\backslash
+stretch{1}}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align center
 [Dedication]
 \end_layout
 
 \begin_layout Standard
+\align center
 \begin_inset ERT
-status open
+status collapsed
+
+\begin_layout Plain Layout
+
+
+\backslash
+vspace*{
+\backslash
+stretch{2}}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset ERT
+status collapsed
+
+\begin_layout Plain Layout
+
+
+\backslash
+phantomsection
+\end_layout
 
 \begin_layout Plain Layout
 
@@ -413,12 +574,52 @@ addcontentsline{toc}{chapter}{Acknowledgements}
 \end_inset
 
 
+\end_layout
+
+\begin_layout Section*
+\begin_inset ERT
+status collapsed
+
+\begin_layout Plain Layout
+
+
+\backslash
+hspace*{
+\backslash
+stretch{1}}
+\end_layout
+
+\end_inset
+
+Acknowledgements
+\begin_inset ERT
+status collapsed
+
+\begin_layout Plain Layout
+
+
+\backslash
+hspace*{
+\backslash
+stretch{1}}
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Standard
 [Acknowledgements]
 \end_layout
 
+\begin_layout Standard
+\begin_inset Newpage newpage
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 \begin_inset CommandInset toc
 LatexCommand tableofcontents