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\documentclass[11pt]{scrreprt}%JB: using a flexible class%\usepackage{geometry}%JB: Only use it if really needed\usepackage[square, comma, sort&compress]{natbib}%\usepackage{amsmath}%\usepackage{amsthm}%\usepackage{amssymb}%\usepackage{amsfonts}\usepackage{mathtools}%JB%\usepackage{delarray}%\usepackage{fancybox}%\usepackage{framed}%\usepackage{multicol}%\usepackage{listings}\usepackage{graphicx}%\usepackage{geometry}%be careful, do not load packages twice%\usepackage{rotating}%\usepackage{wrapfig}%\usepackage{float}\usepackage{subfig}\captionsetup{lofdepth=2}%JB: if you want the subsections in the lof\usepackage{hyperref}\hypersetup{urlcolor=blue, colorlinks=true,citecolor=blue}\begin{document}\title{My thesis work title}\maketitle\tableofcontents % Write out the Table of Contents\listoffigures\chapter{My First Chapter} %%\label{Chapter1}%JB: Your labels should be some kond of mnemonic%JB: A number might change\label{chap:basics}%JB <- for example\section{Indian Ocean Dipole}\label{indianOceanDipole}Strong anti-cyclone south of Sumatra island strengthen by theinfluence of southeasterly wind at Java and easterly wind in TIOcan transfer momentum to southern TIO forcing downwelling rossbywave which moves westward deepening the thermocline leading to