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
private boolean isAutoBuilding() {
		return ResourcesPlugin.getWorkspace().getDescription().isAutoBuilding();
	}
	
	private void buildProjects(IProgressMonitor progressMonitor) {
		Set builtProjects= new HashSet(10);
		Iterator iter= fJarPackage.getSelectedElementsClosure();
		while (iter.hasNext()) {
			IProject project= null;
			Object element= iter.next();
			if (element instanceof IResource)
				project= ((IResource)element).getProject();
			else if (element instanceof IJavaElement)
				project= ((IJavaElement)element).getJavaProject().getProject();
			if (project != null && !builtProjects.contains(project)) {
				try {
					project.build(IncrementalProjectBuilder.INCREMENTAL_BUILD, progressMonitor);
				} catch (CoreException ex) {
					String message= JarPackagerMessages.getFormattedString("JarFileExportOperation.errorDuringProjectBuild", project.getFullPath()); 
					addError(message, ex);
				} finally {
					
					builtProjects.add(project);
				}
			}
		}
	}
}