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xournalpp
Xournal++ is a handwriting notetaking software with PDF annotation support. Written in C++ with GTK3, supporting Linux (e.g. Ubuntu, Debian, Arch, SUSE), macOS and Windows 10. Supports pen input from devices such as Wacom Tablets.
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I've been using Xournalpp[1] for many years, highlighting books as I read them, adding in text/hand drawn annotations in whitespaces if necessary. Unlike other PDF readers/annotators, it saves a separate file, so the original PDF is untouched. It can also export the annotated PDF as a new PDF with highlights and annotations.
Obsidian[2] also has PDF support, where you can open a markdown document side by side with the PDF to take notes as you read. I think it also lets you highlight the PDF itself.
Emacs I think has a similar feature, via plugins/org-mode(?) to the Obsidian setup.
And of course your typical PDF reader probably has support for highlighting PDFs too, but I find them clunky and they save by exporting a PDF, which can be a bit heavy-handed IMO compared to just saving the annotations/highlights as a separate file as Xournalpp does.
[1]: https://github.com/xournalpp/xournalpp/
