How are you organizing massive numbers of PDFs for a dissertation?

My reference folder has officially become chaos. I have downloaded over a hundred papers at this point, and while I started out organized with labeled folders and annotated notes, it slowly turned into a mix of partially read PDFs, duplicate downloads, and disconnected summaries. Citation managers help to an extent, but they don’t solve the mental overload of trying to synthesize everything into coherent themes. I’m curious what real workflows look like for people who’ve completed large-scale literature reviews recently. Are you relying heavily on reference managers? Are you building thematic spreadsheets? Or is there a system I’m missing that makes this stage less overwhelming?