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 void exportResource(IProgressMonitor progressMonitor, IPackageFragmentRoot pkgRoot, boolean isInJavaProject, IResource resource, IPath destinationPath, boolean isInOutputFolder) {
		boolean isNonJavaResource= !isInJavaProject || (pkgRoot == null && !isInOutputFolder);
		boolean isInClassFolder= false;
		try {
			isInClassFolder= pkgRoot != null && !pkgRoot.isArchive() && pkgRoot.getKind() == pkgRoot.K_BINARY;
		} catch (JavaModelException ex) {
			addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.cantGetRootKind", resource.getFullPath()), ex); 
		}
		if ((fJarPackage.areClassFilesExported() &&
					((isNonJavaResource || (pkgRoot != null && !isJavaFile(resource) && !isClassFile(resource)))
					|| isInClassFolder && isClassFile(resource)))
			|| (fJarPackage.areJavaFilesExported() && (isNonJavaResource || (pkgRoot != null && !isClassFile(resource))))) {
			try {
				progressMonitor.subTask(JarPackagerMessages.getFormattedString("JarFileExportOperation.exporting", destinationPath.toString())); 
				fJarWriter.write((IFile) resource, destinationPath);
			} catch (IOException ex) {
				String message= ex.getMessage();
				if (message == null)
					message= JarPackagerMessages.getFormattedString("JarFileExportOperation.ioErrorDuringExport", resource.getFullPath()); 
				addWarning(message , ex);
			} catch (CoreException ex) {
				String message= ex.getMessage();
				if (message == null)
					message= JarPackagerMessages.getFormattedString("JarFileExportOperation.coreErrorDuringExport", resource.getFullPath()); 
				addWarning(message, ex);
			}
		}					
	}
	private void exportClassFiles(IProgressMonitor progressMonitor, IPackageFragmentRoot pkgRoot, IResource resource, IJavaProject jProject, IPath destinationPath) {
		if (fJarPackage.areClassFilesExported() && isJavaFile(resource) && pkgRoot != null) {