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
else
							pkgRoot= jProject.findPackageFragmentRoot(resource.getFullPath().removeLastSegments(1));
					} catch (JavaModelException ex) {
						addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.javaPackageNotDeterminable", resource.getFullPath()), ex); 
						return;
					}
				}
			}
			
			if (pkgRoot != null) {
				leadSegmentsToRemove= pkgRoot.getPath().segmentCount();
				if (fJarPackage.useSourceFolderHierarchy()&& !pkgRoot.getElementName().equals(pkgRoot.DEFAULT_PACKAGEROOT_PATH))
					leadSegmentsToRemove--;
			}
			
			IPath destinationPath= resource.getFullPath().removeFirstSegments(leadSegmentsToRemove);
			
			boolean isInOutputFolder= false;
			if (isInJavaProject) {
				try {
					isInOutputFolder= jProject.getOutputLocation().isPrefixOf(resource.getFullPath());
				} catch (JavaModelException ex) {
					isInOutputFolder= false;
				}
			}
			
			exportClassFiles(progressMonitor, pkgRoot, resource, jProject, destinationPath);
			exportResource(progressMonitor, pkgRoot, isInJavaProject, resource, destinationPath, isInOutputFolder);
			progressMonitor.worked(1);
			ModalContext.checkCanceled(progressMonitor);