I want to cast my vote for the current JDK7 layout. My effort with the source is exclusively to port it to a proprietary OS. I tend to work off the bundled zip files, not Hg, so I'm concerned the lines between the forests. The advantage to me of having CORBA, JAXWS and JAXP be distinct, identifiable trees is that that code never needs porting - there's no native C code and no platform-specific Java code. I build them once and they just work. Hotspot and JDK however are littered with native code and platform-dependent code, all of which I need to at least examine to see if it needs porting.
Tom Salter