FAQ How do I show/hide files like classpath in the Navigator?
Use the menu for Navigator: the small triangle in the Navigator title bar. Select Filters... and check the type of files you want to hide. This technique also applies to the JDTs Package Explorer.
If your plug-in must store metadata in the project content area, consider adding a filter to this list, using the org.eclipse.ui.ide.resourceFilters extension point. The filter specifies a file name pattern and a Boolean attribute specifying whether the filter should be on by default. As an example, the Java development tools add a filter using this mechanism to hide Java class files generated by the compiler.