I wrote my thesis (not PhD) with Pandoc, Zotero, and the Better BibTeX Zotero extension, and found it very enjoyable. Pandoc lets you use Markdown for content a

I wrote my thesis (not PhD) with Pandoc, Zotero, and the Better BibTeX Zotero extension, and found it very enjoyable. Pandoc lets you use Markdown for content and a LaTeX template for styling.