Thesis latex

1) “Command \c@lofdepth already defined” when using packages subfigure and tocloft

Load the tocloft package with the option subfigure.

\usepackage{subfigure}
\usepackage[subfigure]{tocloft}

Moreover, load the package hyperref last. (This is not related to your current problem, but may give rise to further ones.)

2) \usepackage{graphicx,subfigure}

3) \newpage

\addcontentsline{toc}{chapter}{References}

%\bibliographystyle{IEEEtranN} % {IEEEtranN} 

%\bibliography{reference}

\include{reference}

4) \citep{..., ..., ..., ...}