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3.1m2 the name of the code jar for a plugin appears in two places, the plugin.xml/manifest.mf and the build.properties. It would be good if there was a warning if the value in the manifest.mf does not have an entry in the build.properties. There will be cases where the jar is prebuilt so the build.propreties does not have a source.foo.jar= line. In this case there are to possibilities. Either is an over eager warning or PDE could be even more deluxe and check the expressions on the bin.includes line. Typically it either has the jar name (third copy) or *.jar. I just spent about 30 min trying to figure out why it worked fine when running self hosted but not when built and deployed (I got class not found exceptions everywhere so spent most of my time looking at plugin dependencies, resolved states, ...)
*** This bug has been marked as a duplicate of 34165 ***