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It runs differently because eclipse uses its own ant distribution located in plugins/org.apache.ant_1.9.2. You can check it in Preferences dialog "Ant/Runtime" category. I would try to use "Ant Home..." button and switch eclipse to the same ant distribution you use in command line to get the same result. To debug your ant script set break-point in build.xml on the left ruler using context menu or double click and try "Debug As->Ant build ..." from popup menu on build.xml file in Package Explorer View.