To get a folder from the system filesystem and get all of the .instance files of some particular class in it, instantiated as java objects:

 FileObject myFolder = Repository.getDefault().getRoot().getFileObject ("MyFolder/MySubFolder");
DataFolder df = DataFolder.findFolder (myFolder);
FolderLookup lkp = new FolderLookup (df);
Collection c = lkp.lookup (new Lookup.Template (SomeClass.class)).allInstances();