\documentclass[12pt]{report}
\usepackage{mystyle}
\usepackage{subfiles}


\begin{document}

\subfile{./tex/front-matter}
\subfile{./tex/introduction}
\subfile{./tex/engineering}
\subfile{./tex/background}
\subfile{./tex/prototypes}
\subfile{./tex/case-study-fourth-year-system}
\subfile{./tex/case-study-research-ide}
\subfile{./tex/platform}
\subfile{./tex/conclusion}

\include{./tex/citations}

% Add appendices now.
\appendix

\subfile{./tex/appendix-use-cases-1}
\subfile{./tex/appendix-use-cases-2}
\subfile{./tex/appendix-framework-research}

%\chapter{Extra Simulation Results}
%
%\chapter{Review of Linear Algebra}

\end{document}

\documentclass[12pt]{report}
\usepackage{mystyle}
\usepackage{subfiles}


\begin{document}

\subfile{./tex/front-matter}
\subfile{./tex/introduction}
\subfile{./tex/engineering}
\subfile{./tex/background}
\subfile{./tex/prototypes}
\subfile{./tex/case-study-fourth-year-system}
\subfile{./tex/platform}
\subfile{./tex/case-study-research-ide}
\subfile{./tex/conclusion}

\include{./tex/citations}

% Add appendices now.
\appendix

\subfile{./tex/appendix-use-cases-1}
\subfile{./tex/appendix-use-cases-2}
\subfile{./tex/appendix-framework-research}

%\chapter{Extra Simulation Results}
%
%\chapter{Review of Linear Algebra}

\end{document}

Move platform before research IDE
Move platform before research IDE
