In the Java API, I need to add <uses> for the stdout file in addition to <stdout>, otherwise my stdout file won't be transferred because I can't set transfer=true on <stdout>.

Another issue is, if I do setStdout() before uses(), then my transfer=True for uses() is ignored. If I do it the other way, then it works.

I think we need to make it so that either a) we can set transfer and register on stdout, or b) we treat stdout and uses as completely different things.