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Bug 160133 (at this point unresolved) describes the issue. In PDE, bundle projects differ on disk from what they will look like when exported to a jar and bundle.getEntry in Equinox does not account for this difference. It fails to find classes and other resources that are in the bin path of the bundle project. To support ease of development in PDE, Gemini JPA should support locating classes and other resources in the bin path identified in the Eclipse .classpath file.
Created attachment 183718 [details] Patch to support .classpath defined bin path
Patch applied in SVN TX 85.