For example, what do you need to do after you export a pdf of extracted data in general? Do you send the pdf to a Windows device? Currently Marginnote exports a flattened pdf copy, so for the time being you may need to export the excerpt information separately, e.g. export the excerpt to Word, where the hierarchical structure of your organization will be kept in Word in the form of an outline for your summary.
As we (myself, @xurc, @chai46, @JKF, @Spoon, @DrJJWMac, et al) have asked before, the workflow is that we want to save PDF files that are not flattened, i.e., we want PDFs with proper annotations that can be used with other PDF apps like Acrobat, PDF Expert, etc., etc.
Basically, we are just asking for standard support for PDF annotations, as described in § 8.4 “Annotations” of Adobe’s PDF Reference , v. 1.7.
To be honest, I’m not sure why we need to explain this in further detail. There are already quite a few posts on this forum about this issue.
Personally, I don’t use MS-Word and I don’t want MS-Word files. I only want proper PDF files or perhaps RTF files for interchange.
As it stands now, MarginNote does not really support this aspect of the PDF specification, and thus cannot inter-operate with other applications that handle PDF annotations. This lack of inter-operability with other apps has been a significant issue with MarginNote.
If the issue is how to encode MarginNote notes, which have a title and comments, you could use simple markup, i.e., # to represent note titles, etc. Add preferences to control the export formatting, if necessary.
My general request would be: please consider inter-operability a priority. I do not care at all about handwriting support, improved mind map, etc.