(Un-)fortunately, we started in a place where we already had plaintext-ish documentation (we never started with PDFs), so we were converting text to PDFs, not the other way around.
People edit the files in markdown and "publish" them in pdfs.
Generally, we do comments in a combination of google docs views of the PDFs (not-preferred, because they die with the document version) and our code review system (preferred, because they live forever, but unfortunately exclusive to engineers).
I actually don't know to what extent pandoc supports the conversion of existing PDFs with comments to markdown, but that sounds like a really hard problem!
The way I'd move from your situation to mine, is to say "no more comments in pdfs", convert the manuals to plaintext at once, make a comment-less PR of the plaintext manual to the repo, and then hack the comments in as comments on the PR, in a way that depends on your code revision tool.
This might be very hard depending on your CR tool.
Let me know if you have any more specific questions, though, I'm happy to help.
(Un-)fortunately, we started in a place where we already had plaintext-ish documentation (we never started with PDFs), so we were converting text to PDFs, not the other way around.
People edit the files in markdown and "publish" them in pdfs.
Generally, we do comments in a combination of google docs views of the PDFs (not-preferred, because they die with the document version) and our code review system (preferred, because they live forever, but unfortunately exclusive to engineers).
I actually don't know to what extent pandoc supports the conversion of existing PDFs with comments to markdown, but that sounds like a really hard problem!
The way I'd move from your situation to mine, is to say "no more comments in pdfs", convert the manuals to plaintext at once, make a comment-less PR of the plaintext manual to the repo, and then hack the comments in as comments on the PR, in a way that depends on your code revision tool.
This might be very hard depending on your CR tool. Let me know if you have any more specific questions, though, I'm happy to help.
I'll also add contact info to my profile. :)