[phenixbb] --unused_ok, .def, documentation,...

[Ralf W. Grosse-Kunstleve]

Hi Carsten,

> Could you please NOT do this. With your current frequent upgrade cycle
> and the concurrent renaming of options it is very frequent that we need
> to use the unused_ok option. Otherwise it is really a pain to pick up a
> refinement from a couple of weeks ago, just because I needed to upgrade
> phenix in order to get something working. Everybody should understand
> that the unused_ok option is the price you have to pay for frequent
> update cycles.

OK, thanks for the feedback. -- Another simple idea, with the aim
to avoid the --unused-ok in most cases, so that people don't get
too used to doing something potentially dangerous: we could change
phenix.refine to write out only the diffs to the .def file. Given the
same phenix.refine version, there would be no change in behavior when
the .def file is used. When moving to a new phenix.refine version,
chances of stumbling over a change in parameter names are greatly
reduced, so it should be much less likely that the --unused-ok option
is necessary.

I'll add the version tag to the .eff and .def files sometime soon.

Ralf