Integration radius: default r1=4, CLI flag, PixelRefine shares the knob

Bumped the default signal-box radius to r1=4 (r2=6, r3=8): on the lysozyme jet
(1% DMM) it lifts CCref 50.1->52.2% and CC1/2 90.8->92.5% (its broadened spots
spill past a radius-3 box), is neutral on the mono crystal and on the classical
integrator. Added 'jfjoch_process --integration-radius <r1|r1,r2,r3>' (a single
value derives r2=r1+2, r3=r1+4) and wired PixelRefine's shoebox radius to
BraggIntegrationSettings::GetR1() so it shares the classical integrator's knob.

(Explored but rejected: an elliptical/anisotropic Term-2 profile. The jet's
tangential spots are mildly anisotropic - axis ratio 1.15->1.44 low->high res,
azimuthal mosaic, separate from the radial DMM bandwidth - but using the measured
2x2 covariance as the profile DEGRADED the jet, CC1/2 92.5->83.5: the tight
measured width loses to a generous aperture, same lesson as the radius bump.)

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

image_analysis/IndexAndRefine.cpp

@@ -446,6 +446,9 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     if (const auto bw = experiment.GetBandwidthFWHM())
         prd.bandwidth = bw.value() / 2.3548; // FWHM -> sigma
 
+    // Signal-box radius from the shared integration setting (same knob as BraggIntegrate2D).
+    prd.shoebox_radius = static_cast<int>(std::lround(experiment.GetBraggIntegrationSettings().GetR1()));
+
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
     switch (image.GetMode()) {