docs: reorganize configuration.md for better readability
- Add Table of Contents with clear navigation structure
- Reorganize sections into logical groups:
- Getting Started (File Locations, Quick Start Example)
- Core Concepts (Agents, Categories, Model Resolution)
- Task System (Background Tasks, Sisyphus Agent, Sisyphus Tasks)
- Features (Skills, Hooks, Commands, Integrations)
- Advanced (Runtime Fallback, Hashline Edit, Experimental)
- Reference (Environment Variables, Provider-Specific)
- Improve section headers and descriptions
- Add cross-references within document
- Maintain all original content without omissions
- Add clarifying comments to Quick Start Example
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