When you are ready to compile your thesis in the main template, you go to chapter 3, which is where you will begin inserting your chapters. Then delete the contents of the chapter 3 page, which is there only for instruction purposes. Then you proceed to insert each chapter as instructed in the guide. As each chapter file is inserted, the chapter numbers will automatically change. So, your chapter 1 file will become chapter 3 in the main document when inserted. Your chapter 2 file will become chapter 4 when inserted, and so on.
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