The current markdown export file is not very useful if we wish to repurpose those notes as they still have Agenda link dependencies.
I would request if the wikilinks are formated as [[wikilinks]] in an export file. This way, the export files can be more easily used in other apps such as iA Writer, Obsidian, Roam, Logseq and many other tools.
The issue here is what the links should refer to, i.e. do we assume a flat file system where all notes are assumed to be in the same directory? What would the link be if you say have a note Work (Category) > Project X → Note A that contains a link to Personal (Category) > Project Y → Note B ?
I agree, it is slightly tricky and there will be edge cases with handling the links.
In the above scenario, I would just keep it simple, and have the exported Note A contain the text …. [[Note B]] …. When I export “Note B” to markdown as well, I can drop both these files (Note A and Note B) into Obsidian/iA Writer and the links will work.
Obsidian, or Roam or Craft do not care about the file/folder path as much - if I click [[Note B]], it will search for a this note in the entire vault, and open Note B even if that note is in a different directory.
This is also very similar to how Craft markdown exports work - they remove all of their internal Craft links, convert it to wikilinks before creating a markdown export when exporting all notes. There are still several cases, where these links are not always working corrently in Obsidian or Roam, and need some manual fixing, but most of the links work fine.
Maybe just a simple option to pick Agenda internal links, or wikilinks would be awesome 
By the way, thanks for continuin to update Agenda.
I stopped using it towards the end of 2019. I tried it again recently, and with all the new changes I’m back to using it daily.