2MD VS remarks

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In reMarkable's stock output, highlighted text is not textured with PDF annotations, and so its highlights are not readable by any PDF client. You would still need to use third-party software for that. The only two I know of are RCU and remarks.

Which firmware are you on? For 2.15 and below, there are a couple tools that will export real PDF highlight annotation. I use (and am the author of) RCU, which can export both PDF highlights and layers, but there is also remarks if you are comfortable with something more hacky.

But this is only half of the story, these files do not contain highlights or scribbles. That is where another open-source library comes into play, remarks see here.

I had the same problem and although there are tools like remarks the idea is to make it automatic and not waste any time fixing anything (or at least for me), for That's why I recommend you use annotator, the plugin is simple but it exports all metadata in plain text.

I use rsync, but not with a cron. Check out https://github.com/lucasrla/remarkable-utils for an easy implementation of rsync. If you want to mark up pdf files and then get your annotations, check out https://github.com/lucasrla/remarks

I use https://github.com/lucasrla/remarks, which OCRs your highlights to extract what exactly was highlighted, and also outputs screenshots of all pages on which I wrote notes.

This way I can go through my annotations sequentially, save highlights / their main ideas, and reformulate my notes into plaintext a bit more clearly.

With software that can insert/export PDF highlight annotations, like remarks or my own RCU, you may then use Zotero to extract these highlights. This used to be part of a plug-in called Zotfile, but IIRC this can now be done in Zotero directly.

On a side note, thank you for mentioning RMRL! I'd been using remarks, but it has a number of shortcomings, most of which are not present in RMRL.