Compiling with multiple sources on NB 4.0

I'm getting used to the new NetBeans 4.0 interface.  I'm doing some 
complicated things with my build process, so I need to use freeform 
projects.

One of the things I'm doing is using four different directories to store 
my source in.  The reason for this is that there are multiple stages in 
my build process, some of which will cause code to be auto generated.  
Some classes need to be generated before this auto code is generated, 
while others depend on the auto generated code and must be compiled later. 

Unfortunatley, NB 4.0 seems to assume that only one source tree is used 
for things like compiling, running or debugging a single file.  I've 
been able to implement all three of these things for freeform projects 
with a single source root, but not with multiple roots.

Is there a way around this aside from updating my project.xml file 
everytime I need to run or debug a file from a different source directory?

Mark McKay