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https://www.liquidtext.net/ is unique in its feature set and use of gestures and stylus.

It’s definitely worth trying.

I use GoodReader. I'm open to trying something else, but it has folders, bookmarks, annotations, the basics. It lacks all of the fancy stuff in the linked program, though.

PDF reading is the main use I have for a 13 iPad, and I do enough of it that it justifies the device.

Another vote for GoodReader

Did you try the Google Scholar PDF reader? It makes citations clickable (sometimes)

I work a lot with academic papers on iPad and PDF expert is the best! https://pdfexpert.com/

The author is trying to make a version for Android and iOS. The Android version is almost ready, but they're having trouble with the iOS version.

I have used MarginNote and Notability in the past. Take a quick look to see if they do what you want with PDF's.