FileNavigator, using tango, works with the file servers at my school. I managed to establish a connection to the file server and download a few files to my iPad. FileNavigator however did not have an upload feature (or at least one that I could find), so I don't know if that works.

File Navigator (or at least the lite version) uses Tango, a lightweight free library that I think only requires you to display a copy of the licenc (https://github.com/38leinaD/tango)

Does this work with MultiMarkdown as well?