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
return Collections.EMPTY_LIST.iterator();
			reportPossibleCompileProblems(file, hasErrors, hasWarnings, canBeExported);
			IContainer classContainer= outputContainer;
			if (pathInJar.segmentCount() > 1)
				classContainer= outputContainer.getFolder(pathInJar.removeLastSegments(1));
			if (fClassFilesMapContainer == null || !fClassFilesMapContainer.equals(classContainer)) {
				fJavaNameToClassFilesMap= buildJavaToClassMap(classContainer);
				fClassFilesMapContainer= classContainer;
			}
			ArrayList classFiles= (ArrayList)fJavaNameToClassFilesMap.get(file.getName());
			if (classFiles == null || classFiles.isEmpty()) {
				String msg= JarPackagerMessages.getFormattedString("JarFileExportOperation.classFileOnClasspathNotAccessible", file.getFullPath()); 
				throw new CoreException(new Status(IStatus.ERROR, JavaPlugin.getPluginId(), JavaStatusConstants.INTERNAL_ERROR, msg, null));
			}
			return classFiles.iterator();
		}
		else {
			
			List binaryFiles= new ArrayList(1);
			IFile cpFile= outputContainer.getFile(pathInJar);
			if (cpFile.isAccessible()) {
				if (!cpFile.isLocal(IResource.DEPTH_ZERO))
					cpFile.setLocal(true , IResource.DEPTH_ZERO, progressMonitor);
				binaryFiles.add(cpFile);
			}
			else {
				String msg= JarPackagerMessages.getFormattedString("JarFileExportOperation.resourceOnCasspathNotAccessible", cpFile.getFullPath()); 
				throw new CoreException(new Status(IStatus.ERROR, JavaPlugin.getPluginId(), JavaStatusConstants.INTERNAL_ERROR, msg, null));
			}
			return binaryFiles.iterator();