For my university essays, I keep my research citations in Zotero and write in Markdown using Ulysses. Then when it is ready to submit, I'll use Raphael Kabo's technique [1] to export into Microsoft Word. It is a truly simple workflow to get perfect formating with little effort.
Genuine question: what do you do with Word docs sent back to you as email attachments with track changes and embedded comments?
I'm slowly realising that my colleagues for whom this "works" are never going to change. Our shared folders are littered with "Copy of FINAL final + comments 2.7.18-my-copy.docx.docx". It doesn't matter how slick my git + markdown + pandoc workflow is when conversations go like this:
Comments might be extractable, I'm not familiar with docx format but it's zipped X(?)ML type data so there will be parsers. Or a conversion to an intermediate format that's more amenable to computer processing, perhaps.
The problem remains in reverse, though: it's expected that I will produce Word docs full of track changes edits.
I second this workflow - thanks to Zotero and Ulysses I felt I was able to keep track of research for my thesis and easily restructure as I went along. My editor on the other hand was not so happy when I thought it was a good idea to use MS Word's built-in citation tool.. he made me pull them all out and add them back in manually. A good lesson to chat with your editor first before trying to be efficient.
Zotero's cross-platform plugins meant I could use any device for reading and not worry that if I followed important links I'd never find them again.
[1] http://raphaelkabo.com/blog/posts/markdown-to-word