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
for (int i= 0; i < dirtyEditors.length; i++) {
				if (dirtyEditors[i].getEditorInput() instanceof IFileEditorInput) {
					IFile dirtyFile= ((IFileEditorInput)dirtyEditors[i].getEditorInput()).getFile();
					if (selection.contains(dirtyFile)) {
						unsavedFiles.add(dirtyFile);
						addError(JarPackagerMessages.getFormattedString("JarFileExportOperation.fileUnsaved", dirtyFile.getFullPath()), null); 
					}
				}
			}
			if (!unsavedFiles.isEmpty())
				return false;
		}
		return true;
	}
	protected void saveFiles() {
		
		if (fJarPackage.isManifestSaved()) {
			try {
				saveManifest();
			} catch (CoreException ex) {
				addError(JarPackagerMessages.getString("JarFileExportOperation.errorSavingManifest"), ex); 
			} catch (IOException ex) {
				addError(JarPackagerMessages.getString("JarFileExportOperation.errorSavingManifest"), ex); 
			}
		}
		
		
		if (fJarPackage.isDescriptionSaved()) {
			try {
				saveDescription();