Feature/clusterdynamics ml saxs

[kewh5868]

Summary

This PR delivers a broad update across ClusterDynamics, ClusterDynamics ML, and the SAXS workflow/UI. It adds the new ClusterDynamics and ClusterDynamics ML application surfaces, improves predicted-structure generation and analysis, expands SAXS project setup/prefit/DREAM/reporting support, and refreshes the related docs and tooling.

What Changed

ClusterDynamics / ClusterDynamics ML

• Added standalone clusterdynamics and clusterdynamicsml packages, CLIs, and UIs.
• Renamed ClusterDynamics AI to ClusterDynamics ML throughout the codebase, package paths, and user-facing strings.
• Added saved dataset/export support for ClusterDynamics ML results.
• Improved predicted larger-cluster generation, weighting, history tracking, histogram behavior, SAXS overlays, and representative structure exports.
• Improved geometry-aware prediction behavior by learning bond, angle, coordination, and non-node contact statistics from the reference structures.

SAXS

• Expanded Project Setup, Prefit, and DREAM workflows and UI support.
• Updated SAXS plotting, distribution handling, prior-weight/project-manager wiring, and report generation.
• Added model-report support, beam-geometry presets, branding assets, and solution-scattering estimator support.
• Refined template/model support and related runtime/reporting helpers.

Docs / Tooling

• Updated docs, navigation, installation references, and user guides.
• Refreshed supporting UI/tool integrations in bondanalysis, cluster, fullrmc, mdtrajectory, and xyz2pdb.

Validation

• Ran pre-commit successfully on all changed files in the three commit buckets.
• Ran targeted ClusterDynamics ML tests:
  • PYTHONPATH=src conda run --no-capture-output -n saxshell-py312 pytest tests/test_clusterdynamicsml.py

Notes

• The work is organized to keep ClusterDynamics/ML, SAXS workflow changes, and docs/tooling updates reviewable as separate logical commits.
• Formatter/import-order updates from the hooks are included in the final diff.

Closes #39
Closes #17
Closes #4
Closes #5
Closes #8
Closes #9