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Seems currently from UI, there is no way to specify the target directory of the compiled classes to some where other than the default location. This feature should be provided from UI. In general, the IDE user should be kept transparent from the underlying building mechanism - be it Ant or anything else.
For "standard Java projects" in 4.0, the compile target directory, ${build.classes.dir}, is fixed as build/classes/ so far as the GUI is concerned. There is no plan to make that a settable GUI option for 4.0. Perhaps in a future release. You can change this property in project.properties, but I would not recommend doing so while the project is open (or even while the IDE is running); the builds will be fine, but some other aspects of the IDE's behavior (code completion etc.) may not be listening for a change in this property and might become confused.