This is a clean version of PhD dissertation of Utrecht University. The structure of these tex files is listed as follows. If you're a PhD student from Utrecht University, you can easily to reuse the whole project to write your own thesis.

.\uuPhD-dissertation-clean
│
├─cover                             
│  └─cover.ai           // already fit for uu's cover requirements
├─fontback
│  ├─Titlepage              // the first side of frontpage
│  ├─Titleback              // the second side of frontpage (cover's explanation)
│  ├─UU_Titlepage           // the first side of next-page
│  ├─UU_Titleback           // the second side of next-page (committee members)
│  ├─Dedication         // uu doesn't need this
│  ├─Abstract           // English version, then Detuch version
│  ├─Publication        // put your paper list here
│  ├─Contents           // include chapter folder
│  ├─Bibliography           // references
│  ├─Acknowledgments        // your bio and acknowledgment
│  └─Colophon               // the content of the last page, statement of thesis style
├─figures
│  ├─chap01             // all images are .eps edited by Adobe Illustrator
│  ├─......                     
│  └─chap07      
├─Chapters
│  ├─1-intro.tex        // main content of thesis
│  ├─.............                       
│  └─7-conclusion.tex
├─Thesis.tex                // defined how to structure the latex project
├─Thesis.pdf                // compiled output, this is your thesis!
├─classicthesis.tex         // keep it, already fit for uu's requirements
├─classicthesis-config.tex          
├─bibliography.bib          // put the references (bibtex) here
└─.gitignore                // already marked the useless files when using git

I use WinEdt to write and maintain this project, and if you are not familiar with Latex grammar, you can use www.uinio.com/Math/LaTex as a handbook to write your Tex document! Hope your thesis writing journey is happy and easy.