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Look at Thesisdown[0] which is a modified bookdown[1] template for a thesis. It’s based on R Markdown[2], so you get R (or other programming languages) in your document that is run when the document is processed.
The authors of R Markdown/Bookdown are working on a newer tool, Quarto[3].
[0] https://github.com/ismayc/thesisdown
I use Zettlr (https://www.zettlr.com) for all my academic writing. It's a Markdown editor that also supports Latex and exports to various file formats including Latex PDF using pandoc.
You can add custom Latex templates (https://docs.zettlr.com/de/academic/custom-templates/) and then compile to PDF. I'm also using Zotero as my citation engine that is supported natively by Zettlr.
Can only recommend it.