I realize now that the make_fragments.pl script option -old_name_format does more than keep the filename format the same. It actually changes the format of the fragment files. I’ve turned that option on by default in make_fragments.pl. I’m guessing fragment_picker is the same, but the make_fragments.pl script is different.
Yes, in general fragment_picker is the same, although from time to time someone adds extra columns on the right side of the file. I presume make_fragments.pl removes them when asked to do so. I don’t think the fact that now the file format is different causes any trouble; it has been extensively tested in ab-initio.