Merge beam-always into rc181: post-refinement fits the lattice in the fixed space group's setting when -S re-seats the reflections

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HVeDQqN9qRD57vnShzTC37

rugnux/RugnuxScaleMerge.cpp

@@ -975,13 +975,22 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
             }
         }
         if (result.consensus_cell.has_value()) {
-            const auto rot = indexer->FinalizeRotationIndexing();
+            auto rot = indexer->FinalizeRotationIndexing();
             indexer->RethrowIndexerError();
             if (rot && rot->axis) {
                 if (geometry_prepass)
                     prepass_result_ = *rot;   // full result (lattice+geom+axis), for the supercell fallback
                 PostRefineSettings prs;
                 prs.crystal_system = rot->search_result.system;
+                // The reflections were re-seated into the fixed space group's setting above, so the
+                // lattice they are fitted against has to go across with them, in the class it is now
+                // held to. Left in the indexer's setting, every index was another reflection's: on a
+                // P-indexed lattice reseated into C2 the held-out residual started 5 orders of magnitude
+                // above the bare run's, the fit never settled and the header's centre error stayed.
+                if (end_msg.reindex_matrix) {
+                    rot->lattice = rot->lattice.Multiply(stored_to_final);
+                    prs.crystal_system = end_msg.rotation_lattice_type->crystal_system;
+                }
                 prs.num_threads = static_cast<int>(config_.nthreads);
                 prs.refine_geometry = true;
                 // Only a pass still at the file's distance can hold it as a hypothesis; a pass