Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/

A pure move. ModelValidation, RigidBodyRefine, RigidBodyGPU, ModelFFT, ModelGrid,
ModelScaling, ModelMaskGPU, ModelScaleGPU and SigmaA - everything that works on an
atomic model - become the JFJochStructureRefinement library, linked by
JFJochImageAnalysis. WriteModel (the placed-model mmCIF/PDB writer) goes to writer/
as its own small JFJochModelWriter target, so JFJochWriter, which a writer-only build
compiles, does not gain a gemmi dependency. Only include paths and CMake lists change.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi

tests/ModelValidationTest.cpp

@@ -18,17 +18,17 @@
 #include <gemmi/solmask.hpp>
 
 #include "../common/Logger.h"
-#include "../rugnux/ModelFFT.h"
-#include "../rugnux/ModelGrid.h"
-#include "../rugnux/ModelValidation.h"
-#include "../rugnux/RigidBodyRefine.h"
+#include "../image_analysis/structure_refinement/ModelFFT.h"
+#include "../image_analysis/structure_refinement/ModelGrid.h"
+#include "../image_analysis/structure_refinement/ModelValidation.h"
+#include "../image_analysis/structure_refinement/RigidBodyRefine.h"
 #ifdef JFJOCH_USE_CUDA
-#include "../rugnux/RigidBodyGPU.h"
-#include "../rugnux/RigidBodyGPUEngine.h"
+#include "../image_analysis/structure_refinement/RigidBodyGPU.h"
+#include "../image_analysis/structure_refinement/RigidBodyGPUEngine.h"
 #include "../common/CUDAWrapper.h"
 #endif
-#include "../rugnux/SigmaA.h"
-#include "../rugnux/WriteModel.h"
+#include "../image_analysis/structure_refinement/SigmaA.h"
+#include "../writer/WriteModel.h"
 #include "../image_analysis/scale_merge/ReindexAmbiguity.h"
 
 namespace {