Documentation Restructure and Expansion

This PR introduces a substantial reorganisation and expansion of the PhEval documentation. The update improves conceptual clarity, navigation, and contributor guidance, while aligning the documentation structure more closely with PhEval’s architecture and plugin ecosystem.

Structural Reorganisation

The documentation has been restructured into clearly defined, purpose-driven sections:

• Getting Started --> installation, setup, and first-run guidance
• Using PhEval --> core workflows and execution patterns
• Utilities --> helper functionality
• Plugins --> runner ecosystem and extension model
• Benchmarking --> evaluation workflows and outputs
• Developer Documentation --> architecture, API reference, and contribution guidance

This structure improves discoverability for new users while making advanced topics more accessible for experienced contributors.

Expanded Developer Documentation

Significant enhancements have been made to support contributors and plugin developers:

• Clearer documentation of runner interfaces and plugin integration points.
• Relocation of the auto-generated API reference into the formal Developer Documentation section for improved cohesion.
• Improved alignment between documentation structure and internal code organisation.

These changes reinforce PhEval’s role as an extensible benchmarking framework.

Utility Documentation Enhancements

Dedicated documentation has been added for key utilities that were previously under-documented:

• Data preparation workflows
• Phenotype scrambling
• Variant utility functions
• Resource update mechanisms

This ensures supporting functionality is clearly described and reproducible.

New and Expanded Content

• Updated installation instructions
• Overview of the PhEval runner ecosystem
• Practical guidance for executing runners
• Clearer explanation of benchmarking outputs and workflow expectations

These additions help bridge the gap between conceptual understanding and operational use.

Documentation Cleanup

• Removal of deprecated or redundant files (e.g., roadmap and style guide)
• Reduction of duplication and outdated instructions
• Standardised formatting and terminology across sections

Visual and Navigation Improvements

• Improved navigation structure and tab support
• Enhanced workflow diagrams and embedded graphics
• Updated styling for improved readability