Here is my template for PhD or other theses, for pdfLaTeX (or LaTeX, but pdfLaTeX provides better internal hyperlinks).
It is based on the memoir class, which has a lot of useful features/options built-in (the documentation for the memoir class says that ‘[it] provides the functionality of over thirty of the more popular packages, thus simplifying document sources’).
If there is any specific typesetting feature you want to use in your thesis, you should first check in the comprehensive manual for the memoir class via the link above (which has a detailed index). It may well be that what you want is already provided by the memoir class (and it is better to use its built-in capabilities, rather than loading additional style files, unless you have to).
Starting from the (unpacked) template, you need to edit the thesis.tex file, to point to all the ‘frontmatter’ you want (titlepage, summary, etc), then your particular chapters and appendices, then the ‘backmatter’ (i.e. references). Note that when drafting, if you want to process one or a few chapters only, edit the ‘\includeonly{...}’ line in thesis.tex as needed.
Many aspects of the style of the thesis are set in thesis.sty, which you can change as you want, and some of the possibilities are explained in the comments in the file. These include: (1) chapter/section styles, (2) page header style, (3) fonts, (4) colours for hyperlinks.
The latest Version is 1.15, dated 2022/07/28.
See alse these notes for instructions for these additional features: 1) redacting selected figures (for the ‘published’ version of the thesis); 2) adding sequential images at the bottom corners of pages, for flip-books.
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