Thanks all. Sorry for the late reply, I've been in transit. Anyhow, the latest suggestion helped, but there are still library problems. And I'm unclear on what @AndyCap means by "all the includes". I think I'm better off waiting until @AndyCap gets back and can take a look at this. I'll happily test drive the new transfer script and Eclipse project file.
In the meantime, I can easily keep myself busy looking into BLE libraries/drivers and see if I can get a basic BLE example working on the Bela image on the Beagleboard. I've done some quick research and it looks somewhat encouraging. If I can get this working and the Eclipse issue gets resolved, it won't be long before I can be contributing rather than taking up the time of the experts here.