yes, that is the idea,
but sorry, i did not test this on RASPBIAN
your description is a little bit poor to see that?
-a- can you try that with a original processing example what NOT use any library
-b- can you confirm that you for export click [linux] and [embed java]
-c- can you make sure that you use the linux way for transport, like .zip of .tar
just copy file to usb stick and copy back might not work with linux app files.
also run from USB drive does usually not work