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After the extra binaries scrambing merge, MDR module does not build anymore when it is part of the moduleconfig if you don't have the scripting module pulled from CVS: E:\brian\projects\netbeans\nb_all\mdr\build.xml:74: E:\brian\projects\netbeans\nb_all\scripting\external not found. Previously, MDR would build just fine without having the scripting module pulled.
This is not a defect. Scripting module is part of standard netbeans distribution. Previously it did not fail because the extra binaries package *did* always contain extra binaries also for scripting module (even if you did not check out the sources). Now you get only binaries of the modules that you have checked out. But anyway, the dependency on the scripting module is there because the mdrshell application needs it. I am now restructuring the MDR a bit (I have created a new autoload module from jmiutils, moved org.netbeans.mdr.shell to org.netbeans.mdrshell and removed building of mdrshell application from the default build target - you will see more info about that today on the mailing list), which should make this problem disappear.