Rugnux live: the uploaded model is refined after placement; refined scores, model, maps and blobs in the status, the viewer and the hero

The live run refines a placed model as `rugnux` does (ProcessConfig::refine), after every decision
and before the end message; a cut before it starts leaves it out, as the model. The writer still
gets the placed model; the refined one stays with the broker.

API (broker/jfjoch_api.yaml):
- rugnux_live_model.refinement (rugnux_live_refinement): performed, reason, on_gpu, seconds, r_work,
  r_free, rmsd_bonds_A, rmsd_angles_deg, blob_count, blobs (at most 50, rugnux_live_blob: kind, x, y,
  z, peak_sigma, volume_A3, nearest_atom, nearest_atom_distance_A)
- rugnux_live_status.refined_model
- /rugnux/model.cif and /rugnux/map.ccp4 take stage=placed|refined, by default the refined model
  where there is one; the anomalous map stays on the placed model's phases (the refined
  coefficients carry none).
Regenerated broker/gen, frontend/src/client, redoc, and the python client docs (which also brings
the hero fields and rugnux_live_model it was missing).

Frontend: the model card keeps its green/red and gets "R-free 0.xx (refined)" as its context line,
"refining..." while the step runs; the model section adds refined R-free and blob tiles; Mol*
shows the refined model and maps, with the blobs as small spheres coloured by reading (switch, off
at first). The Refinement step is in the timeline like any other.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 3b47fb9a53b7dfad1c1ed289e169094c8d3d9d3e)
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leonarski_f committed 2026-10-26 01:38:25 +01:00
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@@ -231,6 +231,9 @@ Class | Method | HTTP request | Description
- [RoiCircleList](docs/RoiCircleList.md)
- [RoiDefinitions](docs/RoiDefinitions.md)
- [RotationAxis](docs/RotationAxis.md)
- [RugnuxLiveBlob](docs/RugnuxLiveBlob.md)
- [RugnuxLiveModel](docs/RugnuxLiveModel.md)
- [RugnuxLiveRefinement](docs/RugnuxLiveRefinement.md)
- [RugnuxLiveStatus](docs/RugnuxLiveStatus.md)
- [RugnuxLiveStep](docs/RugnuxLiveStep.md)
- [RugnuxSettings](docs/RugnuxSettings.md)