I used the web interface to mount a windows share to /media/hdd (shared also with the build machine)
On the build machine: it is a simple 'make' then 'cp'
on the dreambox: 'chmod' then run
I'm not sure if using flash wizard pro has more to offer compared to this method.
I was considering creating a plugin for later distribution, but it seems that a simple binary + a script/howto is more then enough.