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Currently, the user can create a MANIFEST.MF file for an ear project by using the empty file template. It would be nice to create a better template for this (with real manifest data in it).
User should be able to add user defined entries to MANIFEST.MF file of all project types - j2se and j2ee - in addition to those entries added by the IDE. This is especially needed for the "Class-Path:" line.
J2EE team support ends, thus returning the issue back.
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss