452 revamp docs

[yaseminbridges]

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.

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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.

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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.

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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.

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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.

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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• Reduction of duplication and outdated instructions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

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Visual and Navigation Improvements

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