leonarski_f 07c8b2ddd4 docs: the Rugnux card and the naming table mention refinement and live collections ...

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit f8d07397288137dd5e3a0e5c101f2036d51228bd)

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_ext

Docs landing page: a real diffraction frame in the hero, and the command with a model

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_static

docs: home page with the three programs, download pages for rugnux and the viewer, technical reference grouped below

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images

docs: refinement's GPU engine in GPU data analysis, refinement in the pipeline figures

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landing

Docs landing page: a real diffraction frame in the hero, and the command with a model

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python_client

Refinement cut by the run's cancel; the hero shows the refined R-work / R-free

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ACKNOWLEDGEMENT.md

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

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BATTERY_REPORT.md

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CBOR.md

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CHANGELOG.md

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conf.py

docs: a standalone front page with the three programs and the downloads, the Sphinx tree one page below it

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CPU_DATA_ANALYSIS_DECISIONS.md

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

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CPU_DATA_ANALYSIS_IMAGE.md

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

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CPU_DATA_ANALYSIS_INDEXING.md

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

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CPU_DATA_ANALYSIS_INTEGRATION.md

docs: serial-stills indexing ambiguity described the same way everywhere

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CPU_DATA_ANALYSIS_REFINEMENT.md

Refinement: common cofactors and modified RNA nucleotides in the embedded dictionary; heme iron restrained from LINK records

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CPU_DATA_ANALYSIS.md

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

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DEPLOYMENT.md

docs: home page with the three programs, download pages for rugnux and the viewer, technical reference grouped below

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DETECTOR_GEOMETRY.md

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DETECTORS.md

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documentation.rst

docs: the Rugnux card and the naming table mention refinement and live collections

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EXTERNAL_TEST_DATA_STILLS.md

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EXTERNAL_TEST_DATA.md

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FPGA_DATA_ANALYSIS.md

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FPGA_DESIGN.md

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FPGA_LICENSE.md

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FPGA_NETWORK.md

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FPGA_PCIE_DRIVER.md

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FPGA_SETTINGS.md

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FPGA.md

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GPU_DATA_ANALYSIS.md

docs: refinement's GPU engine in GPU data analysis, refinement in the pipeline figures

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HARDWARE.md

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HDF5.md

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IMAGE_STREAM.md

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JFJOCH_BROKER.md

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JFJOCH_VIEWER.md

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JFJOCH_WRITER.md

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jfjoch.png

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JUNGFRAUJOCH.md

docs: home page with the three programs, download pages for rugnux and the viewer, technical reference grouped below

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LICENSE.md

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NAMING.md

docs: the Rugnux card and the naming table mention refinement and live collections

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OPENAPI_SPECS.rst

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OPENAPI.md

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PIXEL_MASK.md

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PYTHON_CLIENT.md

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RELEASE_CONTENTS.md

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REPOSITORIES.md

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requirements.txt

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RUGNUX_ADVANCED.md

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RUGNUX_BENCHMARKING.md

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RUGNUX_CALIBRATION.md

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RUGNUX_DOWNLOAD.md

docs: home page with the three programs, download pages for rugnux and the viewer, technical reference grouped below

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RUGNUX_FORMATS.md

docs: rugnux getting-started pages - refinement, the full output list, a troubleshooting note

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RUGNUX_INSTALL.md

docs: rugnux getting-started pages - refinement, the full output list, a troubleshooting note

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RUGNUX_INTEGRATION.md

docs: rugnux options, model and export pages brought in line with the usage text

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RUGNUX_MODEL_AND_REFERENCE.md

docs: rugnux getting-started pages - refinement, the full output list, a troubleshooting note

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RUGNUX_OVERVIEW.md

docs: serial-stills indexing ambiguity described the same way everywhere

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RUGNUX_REPORT.md

rugnux: unit-cell e.s.d.s - ZERR in a new SHELX .ins beside the .hkl, _cell.*_esd in the mmCIF, CELL_ESD_* in the report

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RUGNUX_TUTORIAL.md

docs: rugnux getting-started pages - refinement, the full output list, a troubleshooting note

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RUGNUX.md

docs: rugnux getting-started pages - refinement, the full output list, a troubleshooting note

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SECURITY.md

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SOFTWARE_INTEGRATION.md

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SOFTWARE.md

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TECHNICAL.md

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

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TESTS.md

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THIRD_PARTY_NOTICES.md

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

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TOOLS.md

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VERSIONING.md

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VIEWER_DOWNLOAD.md

docs: home page with the three programs, download pages for rugnux and the viewer, technical reference grouped below

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WEB_FRONTEND.md

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