I like GoodReader for this. It’s the only app I’ve found that stores my annotations in the PDF files themselves, and allows me to keep my PDF library in sync ov

I like GoodReader for this. It’s the only app I’ve found that stores my annotations in the PDF files themselves, and allows me to keep my PDF library in sync over SFTP, Dropbox, etc. so that I can read and annotate documents on non-Apple devices as well.