Add script-based workflows for reproducible MSML operations

[rororowyourboat]

Closes #654

Summary

This PR introduces script-based entry points for common MSML workflows, reducing reliance on notebooks for reproducible, automatable operations.

Changes

• ✅ Created directory with CLI tools
• ✅ - Validate MSML specifications (CI-friendly)
• ✅ - Automated report generation
• ✅ Comprehensive with:
  • Usage examples for each script
  • Scripts vs notebooks guidance
  • Recommended project structure
  • Template for new scripts

Benefits

• CI/CD integration: Scripts can be used in automated pipelines
• Reproducibility: Deterministic, versioned workflows
• Batch processing: Process multiple specs automatically
• Testability: Scripts are easier to test than notebooks
• Flexibility: Notebooks remain for exploration, scripts for automation

Usage Examples

Design Philosophy

• Notebooks for exploration: Interactive analysis and visualization
• Scripts for automation: Reproducible, testable, CI-friendly workflows
• Shared modules: Extract reusable logic for both notebooks and scripts

[Copilot]

Pull request overview

This PR introduces script-based entry points for validating MSML specs and generating documentation, plus a README to guide using scripts vs notebooks.

Changes:

• Added scripts/load_and_validate_spec.py to load and validate MSML JSON specs via CLI, suitable for CI and batch validation.
• Added scripts/generate_reports.py to (intended to) generate documentation reports from MSML specs, with CLI options for format and output directory.
• Added scripts/README.md documenting available scripts, usage examples, and guidance on structuring and extending script-based workflows.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 6 comments.

File	Description
scripts/load_and_validate_spec.py	Implements a CLI tool to load specs with load_from_json, report basic counts in verbose mode, and exit non-zero on validation errors, enabling CI-style validation.
scripts/generate_reports.py	Implements a CLI wrapper intended for report generation from specs, but currently only logs status messages and does not actually invoke the reporting functions, and its docstring overstates HTML/Obsidian support.
scripts/README.md	Documents how to use the new scripts, their use cases, and how to structure/add scripts, though it currently overclaims batch reporting capabilities versus the actual generate_reports.py interface.

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[Copilot]

load_from_json is called without the optional spec_path argument, which causes it to print a "Add spec path to load_from_json..." message on every run and prevents spec-tree loading that downstream reporting tools may rely on.
For cleaner CLI output and to support spec-tree-aware reporting (e.g., Obsidian vault generation), consider passing the spec_path into load_from_json rather than using the default.

Suggested change

	ms = load_from_json(spec_data)
	ms = load_from_json(spec_data, spec_path)