Model test continuation

[kewh5868]

Summary

• Expanded Bond Analysis outputs and controls, including dihedral/coordination workflows, richer statistics, plotting/export updates, and UI/CLI coverage.
• Improved Cluster Dynamics startup/project behavior, plotting/export workflows, prediction history handling, and related docs/tests.
• Added SAXS project tooling plus EXAFS GDS mapping workflows, Direct Frame SAXS support, shared plotting/editor improvements, and project-memory/UI refinements.
• Refreshed SAXSShell user-guide navigation and docs for the current project workflows.

Scope Notes

• Deliberately excluded the spectroscopy mapping tool, spectroscopy reference library/scripts/tests, and docs/reference/exafs_gds_mapping/geometric_model.tex.
• Remaining local dirty files are those excluded follow-up items.

Validation

• Pre-commit hooks passed for each local commit after hook-driven formatting/fix retries.
• A broader focused pytest sweep was attempted, but the Qt/runtime-heavy runner became stale before producing a reliable final summary, so it is not counted as completed validation.