`rugnux <images> <model> <reflections>` in any order, without --model or -z. Each positional file
is classified by its contents (RugnuxInputKind.h, in JFJochRugnuxOutput - the library still reads
no files): an MTZ (magic) or an mmCIF with a _refln / _diffrn_refln loop is reference data (-z; the
input itself in --mode refine), a PDB file (a PDB record first, then ATOM/HETATM) or an mmCIF with
an _atom_site loop is a model (--model), anything else is images for the readers. CBF (###CBF or
_array_data) counts as images; a file whose first line is neither data_ nor a PDB record is decided
there, so image files are not read through. An mmCIF holding both atoms and reflections is refused
as ambiguous. At most one model and one reference, --model/--mr and -z included. Gzip read through.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 8f844b0bf86f338d20e8aed426a387722dd8d7cc)
