Course material still arrives as PDF, and the first thing most people do with it is retype the parts they want into their notes. Converting the whole file to Markdown first turns out to be a lot less work.
Markdown keeps the heading structure, so chapters and sections stay navigable, and tables come across as pipe tables you can paste into a spreadsheet. From there the notes live in the same plain text files as everything else, searchable with grep and versionable with git.
The converter I use runs in the browser, so a lecture PDF never leaves the laptop and no account is needed: https://pdf2md.me
Two caveats worth knowing before you try it: scanned handouts need OCR first because there is no text layer to extract, and multi-column layouts sometimes interleave, so it is worth checking the first page of the output before trusting the rest.
Interested to hear whether anyone here has a different workflow for getting readings into a notes system.