Recommendation for PDF "organizer"

I am looking for a PDF library organizer / tool. The requirements are:

1. I can create "shelves" where I could sort the PDFs by topics.

2. I could access it both from my iPad and from my Mac or maybe even the iPhone.

3. If possible (not necessary), there should be an easy way to annotate it on the iPad with the pen.

I never did find quite an organizer like this. I am looking to do it for school papers that I read.

Thank you.

Solution 1:

Have you just tried using iCloud drive on the Mac and the "Files" app on the phone/iPad, with shelves represented by sub-folders?

Apps are opened and marked in Preview on the Mac and in-app markup is allowed in Files.

All changes are synced. Elegant. Free. Baked-in using no extra apps.