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I have a mobile application I created in NB 4.0. I upgraded to the project to 4.1. When I attempted to use the new feature to auto-increment the MIDlet-Version attribute with the ${deployment.number} it didn't work. The actual text "${deployment.number} is put in the jad and the manifest of the jar. In purusing the project files (build-impl.xml?) in nbproject, I noticed that several ant commands around deployment didn't exist in my upgraded project, but do exist in new mobile applications that i create in NB4.1 (the auto-numbering of builds worked with a freshly created project).
Mobility issue.
Your build-impl.xml has to be exactly the same for all upgraded projects as for any new project because the scripts are automatically upgraded. The upgrade may be cancelled if you did some manual modifications to the build-impl.xml. Try to delete the build-impl.xml and re-open the project - it should re-generate the script and solve your problem.
verifying all old issues