Hypothesis Annotation
Hypothesis is conducive to searching (both text, tags and annotations being searchable) as well as for tracking citations and writing papers. Since it's social annotation - it can be private, but also, it can enable students to form study groups and share annotations, questions, related links, etc. with each other - as a web layer on top of the PDF readings. If that is at all of interest, here is more info: https://youtu.be/n--Og_NKAgw?t=13 and the website: https://web.hypothes.is/start/