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See bug329277. In org.eclipse.core.runtime.compatibility.registry we had a case where a classes/ folder (which only contained .class files, not .java files) was included as a source folder: source.runtime_registry_compatibility.jar = src/,\ classes/ This started to cause compile errors when the build moved to a newer version of JDT/Core (I think the upgrade to M3). This bug is being opened to track down what changed in the behavior of JDT/Core to cause this scenario to start failing. We have implemented a workaround in bug329277 to successfully build org.eclipse.core.runtime.compatibility.registry but we should still get to the bottom of why this started to fail.
On the JDT/Core side, this is likely coming from the fact that I used the option -sourcepath to pass in the source path option from the ant task. Before I used to pass them as a classpath entry. So being a source path means that the classes are only search from a source file not a class file. Closing as FIXED.
Verified for 3.7M4 using build I20101206-1800