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
return;
		}
		if (resource.getType() == IResource.FILE) {
			if (!resource.isLocal(IResource.DEPTH_ZERO))
				try {
					resource.setLocal(true , IResource.DEPTH_ZERO, progressMonitor);
				} catch (CoreException ex) {
					addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.resourceNotLocal", resource.getFullPath()), ex); 
					return;
				}
			if (!isInJavaProject) {
				
				try {
					isInJavaProject= resource.getProject().hasNature(JavaCore.NATURE_ID);
				} catch (CoreException ex) {
					addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.projectNatureNotDeterminable", resource.getFullPath()), ex); 
					return;
				}
				if (isInJavaProject) {
					jProject= JavaCore.create(resource.getProject());
					try {
						IPackageFragment pkgFragment= jProject.findPackageFragment(resource.getFullPath().removeLastSegments(1));
						if (pkgFragment != null)
							pkgRoot= JavaModelUtil.getPackageFragmentRoot(pkgFragment);
						else
							pkgRoot= jProject.findPackageFragmentRoot(resource.getFullPath().removeLastSegments(1));
					} catch (JavaModelException ex) {
						addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.javaPackageNotDeterminable", resource.getFullPath()), ex); 
						return;
					}