I’ve mostly followed the setup in the post. The only main difference is that I configured one highlighted colour (Magenta in my case) to identify keywords that I wanted to collect in a separate section. I’ve tweaked the Zotfile setting so that all keywords highlighted in that colour would be given a prefix, which I later removed. Once I have exported the attachment (with zotfile) and created the note (with mdnote), I run a hacky script (written in R because that is the only language I know, but the same can be done in most other programming languages) that edit the md file (e.g. move the comments made on a highlighted section at the beginning of the highgliht rather than at the bottom, gather all the keywords highlighted in magenta in a separate block)
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