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It is odd for the NMW to put the module JAR file in the same package as your source files. Until recently e.g., if you then added your package to the JAR and tried to build, you would get a StackOverflowError! This jarpackager bug has been fixed I think, but we should not push our luck. Better to create it e.g. one directory level up (and name according to the package where sources are going?).
Fixed in main trunk and release32 - RC2 JAR content file will be created in the root directory of target filesystem.
Target milestone -> 3.2
Resolved for 3.3.x or earlier, no new info since then -> closing.