You should wait for the official sdk because the Raven guys seem to have quite changed the BSP format. No, this is not one of those "don't do that it'll get you killed"-threads, I'll just explain:
The first four bytes of a BSP file are the so called magic code, the fifth is the version number. (Just open the map with a Hex editor)
For a normal Q3 map this looks like:
49 42 53 50 46 | IBSP Bsp version 46
But for JO:
52 42 53 50 01 | RBSP Bsp version 1
So I think something totally new has been introduced to the BSP format, otherwise changing the magic code sucks
I chose to post it in here for all those unsuccesful mappers out there.