Build dependencies fix, take 3

[Bryce McKinlay]

This patch fixes CNI headers to depend on their .class file rather than 
libgcj.jar, and also fixes dependency tracking for native files in 
subdirectories. The problem here was that automake was putting the 
dependency files in the top level of .deps, but looking for them in 
subdirectories under .deps. The solution is to do the same thing for the 
native files in subdirectories as wel already do for .java files.

I've tested this with a full parallel build and it seems to work fine, 
so I'm checking it in.

regards

Bryce.


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