Thanks very much. I wasn't sure how to recompile everything, so I deleted it all and started again. I then had several issues with bits of missing software, but eventually I was able to get it going.
"commander takeoff" caused the simulated vehicle to lift off, then go into "failsafe enabled: no datalink". RTL took it straight back down again. I had to start up QGroundControl to give it a datalink!
Anyway, it looks as if I finally have a working toolchain. Thanks again.