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Resolution: Fixed
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I can't seem to get the batch to work just from within one module. I am normally working only in core, and want to rebuild and test only that. If I try to run ant from the core directory it fails with compilation errors. If I got to the daffodil directory then ant works fine and there are no such compilation errors.
Until eclipse is fixed and runs all unit tests in a tree, (or maybe if we switch to junit4 this will just work?...) the batch has to be run frequently, so running just one module will really help.