Here's a great Mac app for getting your PDF annotations into usable text. Highlights (Mac App Store Link) takes the native PDF annotation you probably already use and exports them as annotated Markdown. It's a bit of a text editor and a bit of a PDF highlighter. What I really like is that it automatically captures the page number for each annotation.
Highlights has a basic image selection tool that automatically drops a Markdown image link right into the text area, which adds an entirely new level to annotating in Markdown. It's nice to write some notes but it's awesome to also get an image of the PDF added instantly.
Highlights will also attempt to identify the DOI of a PDF and retirieve the relevant bibliographic data.
It also supports the fancy new TextBundle format for extended Markdown based documents, not to mention several convenient export options.
It's not an overly complicated app but there are some interesting options for working with meta data and tags. So, while being pretty basic, it has considerable power. This is a 1.0 version and has some quirks but it's surprising good at extracting referenced markdown quickly.
It's a pretty clever app. If this is something you need, then Highlights is kind of a game changer.
Highlights 1.0 for Mac | $10