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Draft: Docs - Fix README inaccuracies verified against codebase

wgonzalez requested to merge worktree-readme-accuracy-fixes into main

Audited every claim/command/path in the README against the source and by running the documented CLIs in a sandbox. Fixes:

  • Remove broken CLI viz command (data_visualization.py has no main / argparse and ignores zarr_path/Color); point to the Data Analyzer GUI, run_integration.py --plots, and the XRD.visualization API instead.
  • Document the third GUI tab (Process) in the intro, Windows "Includes", launcher tabs, and Process Data section (was described as two tabs).
  • Complete the Project Structure tree: add the hpc/ run-service + Globus layer, launcher.py, initialize_gsas_headless.py, batch_processor_subprocess.py, and process_tab.py; fix the 2-tab comment.
  • Align Data Organization tree with path_manager.py (Data/{MonthYear}/ {Sample}/{Stage}, Processed .../Intensity, Params/analyzer).
  • Link docs/GLOBUS_REMOTE.md (experimental); note remote HPC as experimental.
  • Reduce Authors section to the two primary authors; standardize v1.1 -> 1.1.0.
  • Broaden image-format list (.tif/.tiff, .edf.GE1-GE5); add batch recipe-path caveat and run_prisma.py --verify note.

Co-Authored-By: Claude Opus 4.8 (1M context) noreply@anthropic.com

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