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
int count= 0;
		for (int i= 0; i < members.length; i++) {
			if (members[i].getType() == IResource.FILE)
				count++;
			else
				count += getTotalChildCount((IContainer)members[i]);
		}
		return count;
	}
	/**
	 * Exports the passed resource to the JAR file
	 *
	 * @param element the resource or JavaElement to export
	 */
	protected void exportElement(Object element, IProgressMonitor progressMonitor) throws InterruptedException {
		int leadSegmentsToRemove= 1;
		IPackageFragmentRoot pkgRoot= null;
		boolean isInJavaProject= false;
		IResource resource= null;
		IJavaProject jProject= null;
		if (element instanceof IJavaElement) {
			isInJavaProject= true;
			IJavaElement je= (IJavaElement)element;
			try {
				resource= je.getUnderlyingResource();
			} catch (JavaModelException ex) {
				addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.underlyingResourceNotFound", je.getElementName()), ex); 
				return;
			}
			jProject= je.getJavaProject();