I’ve been using Scott Selisker’s Scrivener-inspired plain text writing workflow, which relies on the free software tools Zotero and Atom, since starting my PhD. I also take notes in Markdown, the simple markup language that the workflow uses for academic drafting.
I’ve made a few plug-ins to go with this setup and other plain text pursuits:
notes-from-pdf, an Atom package that improves the process of copy-pasting quotations from a PDF into a text file
pandoc-interface-yaml, an Atom package that lets you export to various document formats using the options needed for citation formatting, etc.
wc-tracker, a command line tool and Node.js module for tracking word count changes to one or more documents
rpg-dice, an Atom package for making Dungeons & Dragons-style dice rolls directly in a text editor (this one is not so much a boost to the academic writing productivity)