Bug 13799 JAR exporter exports class files from output folder
There was a problem with the output folder not being detected as such.
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/jarpackager/JarFileExportOperation.java
}
			}
			
			if (pkgRoot != null) {
				leadSegmentsToRemove= pkgRoot.getPath().segmentCount();
				if (fJarPackage.useSourceFolderHierarchy()&& !pkgRoot.getElementName().equals(pkgRoot.DEFAULT_PACKAGEROOT_PATH))
					leadSegmentsToRemove--;
			}
			
			IPath destinationPath= resource.getFullPath().removeFirstSegments(leadSegmentsToRemove);
			
			boolean isInOutputFolder= false;
			if (isInJavaProject) {
				try {
					isInOutputFolder= jProject.getOutputLocation().isPrefixOf(resource.getFullPath());
				} catch (JavaModelException ex) {
					isInOutputFolder= false;
				}
			}
			
			exportClassFiles(progressMonitor, pkgRoot, resource, jProject, destinationPath);
			exportResource(progressMonitor, pkgRoot, isInJavaProject, resource, destinationPath, isInOutputFolder);
			progressMonitor.worked(1);
			ModalContext.checkCanceled(progressMonitor);
		} else if (element instanceof IPackageFragment)
			exportPackageFragment(progressMonitor, (IPackageFragment)element);
		else
			exportContainer(progressMonitor, resource);
	}
	private void exportPackageFragment(IProgressMonitor progressMonitor, IPackageFragment pkgFragment) throws java.lang.InterruptedException {