The setup on my laptop:
- Zotero (https://www.zotero.org/) A software that allows you to easily keep references to academic papers right from your browser. Available as standalone app with multiple browser extension, or directly integrated into firefox. When you are on a paper's webpage, clicking on the button extracts its information, its PDF (if available) and do a capture of the webpage and store everything structured. You can then copy citation directly from zotero, generate a bibtex file, or use libreoffice extension. It also allow to sync between computer up to 300M, and extending the storage is quite cheap.
- Zotfile (https://github.com/jlegewie/zotfile) An Zotero extension that monitor the download folder to let you attach downloaded PDF to existing entries. It also rename PDFs with the pattern you want. And the killer feature: It is able to extract what you electronically annotated on the PDF (Highlights, comments)!!
- Okular (https://okular.kde.org/) For reading and annotating PDF. Straightforward use, nice annotations tools (F6 to open, double click items to make them permanent). Ctrl-S to save the annotation to file (otherwise stored somewhere in the user home file).
All these are open source software and are available on Linux!