A mix of things that are constantly changing. I like Polar for reading, storing, and annotating them - but I'm considering moving away from it. I also use Zotero for storing meta data about the papers because it has a really great automatic meta data retrieval [0]. It's also good for searching, sorting and what not based on this info.
My current thoughts are to move more to Zotero because it also has some annotation functionality, but primarily use it as an extraction point to then store these annotations/notes in plain text or markdown. Which then I'll manage with git or something.
I've personally realized it's more important to me to have my notes about the papers easily accessible (hence plain text in git) than to have PDF annotations stored in an app alongside the PDF. I've also realized this has been a little bit of a shift in how I read, making me more focused on extracting information. Not sure how I feel about this yet.
For annotations with zotero, I don't even bother and annotate with the system PDF viewer directly onto the pdf file (preview in my case). Keeps things together all the same for syncing across devices and the annotations are platform independent since it's right on the pdf file. If I need a clean copy I can grab the doi from zotero and download another in like 30 seconds.
