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If you install the nightly build for PHP and look at the Database Explorer, there is no Java DB node. If my memory serves me, this is also the case for Ruby. I am pretty sure that the problem is that derby support is part of the java cluster. It would be nice to fix this, but it is going to require some thought, as currently the Java DB support has some dependencies on elements of the java cluster - I think in order to determine what version of the JDK is running. One solution would be to copy/paste the utility routines that determine the JDK version into the Derby module, and then it won't need to depend on the java cluster any more.
Reassigned to new owner.