For anyone doing academic writing, I use a combination of Logseq, Zotero, and Zettlr. All open source. Collect articles in Zotero. Annotate and take notes on those articles in Logseq with absolutely amazing PDF annotation tools. Write draft in Zettlr which allows me to enter Zotero citations and reference Logseq notes.
Bonus shoutout to LibreOffice for exporting and formatting the final draft. And that’s your recipe for one all-natural, organic, FOSS thesis!
Zotero is such a lifesaver. I started using it to allow for easier citations and reference lists but I've loved being able to keep my sources organized and saved in one place while doing research. The browser extensions are also super convenient to save everything to sort later on.