Bug 11317 Won't export some files to .jar.
Create a new java project called "Foo". In the file system, create a folder named "Foo scripts", and in this folder create a file named "foo.txt". Drag this folder into the eclipse packages view and add it to the "Foo" project. Now try to export the project "Foo" to a .jar file. Only the manifest file shows up, even if the file "foo.txt" is checked!
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/jarpackager/JarFileExportOperation.java
} else if (element instanceof IPackageFragment)
			exportPackageFragment(progressMonitor, (IPackageFragment)element);
		else
			exportContainer(progressMonitor, resource);
	}
	private void exportPackageFragment(IProgressMonitor progressMonitor, IPackageFragment pkgFragment) throws java.lang.InterruptedException {
		Object[] children;
		try {
			children= pkgFragment.getChildren();
			for (int i= 0; i < children.length; i++)
				exportElement(children[i], progressMonitor);
			children= pkgFragment.getNonJavaResources();
			for (int i= 0; i < children.length; i++)
				exportElement(children[i], progressMonitor);
		} catch (CoreException e) {
			
			addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.errorDuringExport", pkgFragment.toString()), e); 
		}
	}
	private void exportContainer(IProgressMonitor progressMonitor, IResource resource) throws java.lang.InterruptedException {
		IResource[] children= null;
		try {
			children= ((IContainer) resource).members();
		} catch (CoreException e) {
			
			addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.errorDuringExport", resource.getFullPath()), e); 
		}
		for (int i= 0; i < children.length; i++)
			exportElement(children[i], progressMonitor);
	}