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I proof read new works and revisions on Kobo.
I use Calibre and Kobo Utilities to copy back the highlight + annotation and info to a window, then copy and paste as a new file in KATE (like Windows Notepad++). The filenames have booktitle & revision. i use sessions (notepad++ or KATE) to have all the files for a project or book or series. I clean up the file to have the structure I want with a couple of regex.
Yes, I'm familiar with various flavours of markdown inc simplest text files that work with MS Word or LO Writer import/copy/paste.
I used to use Jota on Android for additional notes (plain text). Now I use Advanced Notebook in Sage (though I have an Elipsa and had a reMarkable) as it does good on device conversion of pen input (ONLY in the separate Nebo based notebooks) and then I can export plain text or docx (if there is also converted shapes, formula, checkboxes and free hand writing / sketches).
I'm not interested in anything not a calibre plug-in as all kobo content is managed in calibre inc bought books. I do sometimes also annotate PD or bought books. I only sideload ever, on Kindle or Kobo, or other ereaders or apps.
As well as the Kobo Utilities (to copy Kobo highlights & annotations elsewhere and has all the info Kobo saves), calibre has the Annotations, which can read any number of books highlights & annotations into the Calibre database for those books.
I'm not much interested in markdown, nor a standalone application. There is also a configuration option I don't use on Kobo to export to a text file per book.
I can't see exactly what this offers that the three existing popular solutions don't do. I think there is some other program.
I can't see what having Markdown (which flavour?) adds to the original capture (which has to use the touch screen to highlight and touch keyboard to annotate, because there is no pen conversion on the Sage or Elipsa).
There are a few people that don't like calibre, but the Kobo built in option works to export on all models.
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