PixelRefine: make factored Terms 1+2 the model, remove old wiring

PixelRefine is now an intensity-only operation: geometry is fixed (refined
upstream by XtalOptimizer) and the only objective is the factored per-reflection
likelihood (FACTORED_MODEL.md Terms 1+2) - measured per-resolution profile width
R1 plus one Fisher-weighted intensity/scaling residual per reflection, fitting
the per-image scale G and B. Validated on crystal 2 (fixed_master.h5 as stills,
1.7 A): CC1/2 84-92%, CCref 77-92%, flat - reproduces the env-flag prototype and
matches the rotation path from the stills path.

Removed:
- the per-pixel ShoeboxResidual loss and PixelResidual cost functor;
- all in-PixelRefine geometry refinement (orientation/cell/beam/distance/R),
  the regularised-orientation LSQ, signal-weighting, and the global sweep;
- Term 3 (per-spot recentring) - a confirmed no-op on both crystals;
- the diagnostic scaffolding (covariance, centroid, adaptive_R1) and the
  PR_* env knobs + stderr dumps in IndexAndRefine;
- the PredictImage/ChiSquaredImage renderers and the entire viewer
  PixelRefine window/table/params + worker bindings + shoebox overlay.

The sweep box-integrator background median became mean (consistency) by virtue
of removing the sweep. METHODS.md rewritten for the current model; findings
recorded in FINDINGS-2026-06.md. Net -2200 lines.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

image_analysis/IndexAndRefine.cpp

@@ -446,28 +446,6 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     if (const auto bw = experiment.GetBandwidthFWHM())
         prd.bandwidth = bw.value() / 2.3548; // FWHM -> sigma
 
-    // TEMPORARY diagnostic knobs to probe the effect of the (currently fixed) spot
-    // widths R[0] (radial/partiality) and R[1] (tangential/profile). Remove after.
-    if (const char *r0 = std::getenv("PR_R0")) prd.R[0] = std::stod(r0);
-    if (const char *r1 = std::getenv("PR_R1")) prd.R[1] = std::stod(r1);
-    // TEMPORARY: PR_COV refines G,B,R and dumps their per-image correlation matrix.
-    if (std::getenv("PR_COV")) {
-        prd.refine_scale = true; prd.refine_B = true; prd.refine_R = true;
-        prd.compute_covariance = true;
-    }
-    if (std::getenv("PR_FIX_R0")) prd.fix_R0 = true; // hold R0, refine R1 only
-    if (std::getenv("PR_FIX_R")) prd.refine_R = false; // hold R0 and R1: G-B correlation only
-    if (std::getenv("PR_ADAPT_R1")) prd.adaptive_R1 = true; // measure R1 from spot moments
-    if (std::getenv("PR_CENTROID")) prd.measure_centroid = true; // observed-vs-predicted offset
-    if (std::getenv("PR_RECENTER")) prd.recenter_profile = true; // recentre profile on centroid
-    if (const char *s = std::getenv("PR_RECENTER_SIGNIF")) prd.recenter_min_signif = std::stod(s);
-    if (std::getenv("PR_INTENSITY")) { // factored-likelihood Term 1: per-reflection intensity residual
-        prd.intensity_residual = true;
-        prd.refine_orientation = false; prd.refine_R = false;
-        prd.refine_scale = true; prd.refine_B = true;
-    }
-    if (std::getenv("PR_SHAPE")) prd.shape_R1 = true; // Term 2: per-resolution R1 from spot moments
-
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
     switch (image.GetMode()) {
@@ -487,18 +465,6 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
             return false;
     }
 
-    if (prd.covariance_valid)
-        fprintf(stderr, "[cov] GB=%.3f GR0=%.3f GR1=%.3f BR0=%.3f BR1=%.3f R0R1=%.3f\n",
-                prd.corr_GB, prd.corr_GR0, prd.corr_GR1, prd.corr_BR0, prd.corr_BR1, prd.corr_R0R1);
-    if (prd.adaptive_R1)
-        fprintf(stderr, "[R1] %.5f\n", prd.R[1]);
-    if (prd.shape_R1 && std::isfinite(prd.shape_R1_lores))
-        fprintf(stderr, "[shapeR1] lores=%.5f hires=%.5f\n", prd.shape_R1_lores, prd.shape_R1_hires);
-    if (prd.measure_centroid && std::isfinite(prd.centroid_lo_tang_c))
-        fprintf(stderr, "[res] lo_s=%.1f lo_tc=%.3f lo_tp=%.3f lo_rc=%.3f hi_s=%.1f hi_tc=%.3f hi_tp=%.3f hi_rc=%.3f\n",
-                prd.centroid_lo_signif, prd.centroid_lo_tang_c, prd.centroid_lo_tang_p, prd.centroid_lo_rad_c,
-                prd.centroid_hi_signif, prd.centroid_hi_tang_c, prd.centroid_hi_tang_p, prd.centroid_hi_rad_c);
-
     // PixelRefine output flows into the normal save/merge path: the refined
     // geometry/lattice and the already-scaled reflections become the outcome.
     i_outcome.reflections = std::move(prd.reflections);