Finally got koreader and plato set up on my Kobo, and calibre set up for managing and converting ebooks. The default {author}/{title} file structure for moving ebooks to the reader doesn’t work at all for me, but fortunately(?) calibre supports no less than three different template languages allowing for very flexible ebook organisation schemes. These can be configured by opening the “Configure this Device” menu and editing the “Save Template” field.

I ended up using this little script to organise books in a way which makes navigation easy for my collection:

program:
# If the book is in a series, make a folder for that series, and ensure books are in order
# by prepending their series index to their file name.
if (field('series')) then
  strcat(field('series'), '/', field('series_index'),  ' - ', field('title'))
# Otherwise, if a book has tags, make a folder for the first tag and put it there.
elif (list_count(field('tags'), ',') > 0) then
  strcat(sublist(field('tags'), 0, 1, ','), '/', field('title'))
# Otherwise, simply place the book at the top level for easy access and future sorting.
else
  field('title')
fi

A couple of books ended up in the wrong folders, presumably due to some error with tag ordering or metadata syncing, but it was quick to clear up manually in the filesystem.