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 subMonitorTicks= totalWork/10;
				totalWork += subMonitorTicks;
				progressMonitor.beginTask("", totalWork); 
				SubProgressMonitor subProgressMonitor= new SubProgressMonitor(progressMonitor, subMonitorTicks, SubProgressMonitor.PREPEND_MAIN_LABEL_TO_SUBTASK);
				buildProjects(subProgressMonitor);
			} else
				progressMonitor.beginTask("", totalWork); 
						
			fJarWriter= new JarWriter(fJarPackage, fParentShell);
			exportSelectedElements(progressMonitor);
			if (getStatus().getSeverity() != IStatus.ERROR) {
				progressMonitor.subTask(JarPackagerMessages.getString("JarFileExportOperation.savingFiles")); 
				saveFiles();
			}
		} catch (IOException ex) {
			String message= JarPackagerMessages.getFormattedString("JarFileExportOperation.unableToCreateJarFle",  ex.getMessage()); 
			addError(message, ex);
			throw new InvocationTargetException(ex, message);
		} catch (CoreException ex) {
			String message= JarPackagerMessages.getFormattedString("JarFileExportOperation.unableToCreateJarFileDueToInvalidManifest", ex.getMessage()); 
			addError(message, ex);
			throw new InvocationTargetException(ex, message);
		} finally {
			try {
				if (fJarWriter != null)
					fJarWriter.close();
			} catch (IOException ex) {
				String message= JarPackagerMessages.getFormattedString("JarFileExportOperation.unableToCloseJarFile", ex.getMessage()); 
				addError(message, ex);
				throw new InvocationTargetException(ex, message);