Package explorer not showing...packages, in Eclipse. How to fix it?

Do you configure the corresponding folders to be the source folder?

They should be included in the java build path (The project properties--> java build path --> source ) . Eclipse only shows the package structure and provides the necessary stuff such as refactoring capabilities , checking java syntax error for the folders that are included in the java build path.

From the menu pointed in the image, setting Package Presentation as flat may solve your problem.

Edit: Pointed menu is also available in Package Explorer view.

Right Click on your top level of your package, go to build path->use as source folder. Will show you what you want.