When I read pdfs, I upload them to Google Drive and make annotations there. For other stuff, likes on HN and Twitter or snippets emailed to myself makes info persistent. If Nyxt was a browser plugin, I would try it out.
Just curious what PDF annotation tool(s)/setup you use?
After you upload a PDF to Google Drive, you can select text and add comments. That way, you can share the PDF and its comments with collaborators/colleagues etc.