Not the same person but I would suggest using zotero for this purpose. This is one of the best use case of zotero (try zotero 7 beta). Combined with its iPad app you will find it can tick all your requirements.
I recently went back to school and started using Zotero again. Reading and annotating books and papers on iPad, and then having access to all of my notes when writing on desktop is such a simple but amazing feature.
On Linux, I use zathura (but I rarely annotate my PDFs and I use my iPad for that). On macOS, I used Preview (it was good enough) and PDF Expert (Not the subscription version) for editing pages and outline. On the iPad, I begrudgingly use Documents (by readdle).
My PDF are managed by Calibre, but I export various subsets to the file system, so I can find them easily (on the network).
I highly recommend trying out sioyek (as a zathura replacement). it has a bunch of features that make it even more suitable for consuming technical papers/textbooks - such as a significantly faster search & index, an auto generated table of contents, highlights, and portals.
elashri|1 year ago
halgir|1 year ago
I recently went back to school and started using Zotero again. Reading and annotating books and papers on iPad, and then having access to all of my notes when writing on desktop is such a simple but amazing feature.
skydhash|1 year ago
My PDF are managed by Calibre, but I export various subsets to the file system, so I can find them easily (on the network).
umbra07|1 year ago
umbra07|1 year ago