[ec2y]

This is going to sound old school, but I keep things nicely organized with OneNote2016. (A version that still allows you to keep the files on Dropbox, rather than having to deal with the inferior MS cloud.)

What I like is the fact that there is intuitive structure, with (project) notebooks, folders and pages. That makes it easy to add external content and then make notes, although for true annotation, you probably want to manually copy webpages into OneNote, rather than the PDF-style print to OneNote.