docs: refinement chapter (§15), REFINE_ report keys, acknowledgements and in-source credits

- New docs/CPU_DATA_ANALYSIS_REFINEMENT.md (§15): the ML amplitude target and its FFT gradient,
  scale/robust fit/fine solvent mask, D and the variance (work/free), the embedded Monomer Library
  subset and topology, geometry/metal/KL-B restraints, the minimiser, the weight trials, refined maps,
  blobs, GPU/CPU, and a "Not yet" list; with its own References. Linked from TECHNICAL.md and
  CPU_DATA_ANALYSIS.md; §14 no longer says the structure is never refined.
- RUGNUX_REPORT.md: a Refinement (REFINE_*) section - every REFINE_ and REFINE_SCORE_ key, the
  --mode refine input keys and the _blobs.json fields.
- RUGNUX_MODEL_AND_REFERENCE.md: "What it does not do yet"; RUGNUX_ADVANCED.md: --model mentions the
  refinement, --no-refine as in the usage, a --mode refine options table; GPU_DATA_ANALYSIS.md: the
  refinement's CUDA engines and the missing Metal path.
- ACKNOWLEDGEMENT.md: Brunger, Karplus & Petsko 1989 (gradient-balanced starting weight), Nocedal 1980
  (two-loop recursion), Charbonnier et al. 1997 (pseudo-Huber), Jiang & Brunger 1994 (flat solvent
  mask), Kullback & Leibler 1951; all DOIs checked against Crossref.
- In-source credit lines: the weight balancing (replacing a "Brunger (1992)-style" line that named the
  R-free paper), Nocedal 1980, Charbonnier 1997, Jiang & Brunger 1994, Emsley et al. 2010 at
  FindDensityBlobs, Read 1986 at the refined maps. Comments only.
- docs/THIRD_PARTY_NOTICES.md regenerated from the root file with update_version.sh's own step (it
  lacked the CCP4 Monomer Library row).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 09375dba351bae0cc73e9a6f0f79455dc92b3a10)

image_analysis/structure_refinement/Refinement.cpp

@@ -756,8 +756,8 @@ void RefinePlacement(Context &ctx, bool group_b, RefinementResult &result) {
 
 // The X-ray weight that balances the two gradients: the norm of the geometry's gradient (taken on the model
 // shaken by 0.1 A, where a refined model's geometry would have none) over the norm of the X-ray target's.
-// Following Brunger (1992)-style gradient balancing as phenix.refine starts its weight search (Afonine et al.
-// (2012) Acta Cryst. D68, 352-367)
+// Following Brunger, Karplus & Petsko (1989) Acta Cryst. A45, 50-61, as phenix.refine starts its weight search
+// (Afonine et al. (2012) Acta Cryst. D68, 352-367)
 double BalancedWeight(Context &ctx, const std::vector<int> &refinable) {
     std::vector<std::array<double, 4>> gx, gr;
     ctx.engine->Evaluate(ctx.Model(), &gx);
@@ -801,6 +801,7 @@ double BalancedADPWeight(Context &ctx, const RestraintSet &b_restraints, const s
 
 // The model's map coefficients and its difference map, weighted by the refinement's own likelihood: m its figure
 // of merit and D its D (2mFo - DFc, mFo - DFc).
+// Following Read (1986) Acta Cryst. A42, 140-149
 void MakeMaps(Context &ctx, const std::vector<MergedReflection> &merged, double wavelength_A, RefinementResult &result) {
     const RefinementStage stage("maps");
     ctx.Refit();