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Create an SE JPA project (no EE module). There is no way to get a jar file ref to resolve to a jar file within your project. The resolution mechanism uses the virtual file API, which is added with the module core project nature, which is only added with EE modules. That said, I'm not even sure *how* an SE project should use jar file refs. I need a good use case for creating an SE application with external jar refs.
Targeting to Juno release.
I would guess this is a regression from the removal of utility project in Indigo?
It could be considered a regression if there *were* SE use cases before. I'd like to see an SE use case with jar refs before I'd say that for sure, though.