I cannot read a maths book or paper without writing on it.
Microsoft OneNote is cloud-based with syncing, has drawing tools, OCR for image content, handwritten comments, and even a Maths editor, and can organize your stuff. There might even be a symbolic calculator buried somewhere in it. I use it on a Surface Pro; to make the handwritten annotation part work well you really need the Wacom Stylus.
There are a bunch of PDF readers on the PC and Mac which can annotate. I think they all export the annotated PDF, and a couple of smart folders or Google Drive might be enough to maintain a synced system.
Unfortunately, this whole area is one where proprietary is ahead of open source - OneNote and InkSeine are masterworks.