[gxonatano]

1-5. Org mode, with plugins org-roam, org-roam-bibtex, org-noter, and org-citar. Every book I read has an accompanying bibtex file, and a linked note in org-roam. Usually it's an ebook, in which case there's an accompanying PDF as well. Org-roam keeps the book note linked to my other concept notes, org-roam-bibtex and org-citar help keep it connected to the bibtex data, and org-noter keeps my page-level annotations aligned with the page where I'm taking the notes. 2. Org-capture. When I'm on a web page, or in a code editor, or a PDF, I run org-capture and it stores a link to that URL, code location, or PDF page. 3. Very often. 4. Same: org and org-roam. 5. I guess syncing between devices is the thing I find most challenging, but it's not that big of a deal.