GPU_DATA_ANALYSIS.md: the refinement section at the level of the other engines - density gather,
cuFFT r2c/c2r, compose + likelihood target, CSR adjoint, warp-per-atom gradient, restraints and
slot gather, fine mask and robust scale fit (on-device median), reductions and determinism,
stream priority and blocking-sync waits, trial slots over cards, DeviceBytes budget, CPU fallback,
no Metal; indicative RTX 5080 timings.
Pipeline figures: a dashed Refinement box after Structure & map on both, the model branch labelled
as deciding nothing; the stills row gains the indexing-ambiguity step before the first merge.
RUGNUX_OVERVIEW.md: captions, a refinement paragraph, refined outputs under Write.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 8645fb2aca1abbbddec29cdfa99056471f8f38a5)
leonarski_f
0cc3129650
