refactor: Organize Scripts Directory Structure

[aygp-dr]

The scripts/ directory contains 40+ shell scripts without clear categorization, making it difficult to navigate and maintain.\n\n## Current Issues\n- Flat directory structure with many scripts\n- No clear organization by function\n- Difficult to find specific scripts\n\n## Proposed Structure\nscripts/\n- setup/ # Environment and installation scripts\n- analysis/ # Analysis and reporting scripts\n- maintenance/ # System maintenance scripts\n- templates/ # Template management scripts\n- utils/ # Utility scripts\n\n## Implementation Steps\n1. Create new directory structure\n2. Categorize existing scripts\n3. Move scripts to appropriate directories\n4. Update documentation and references\n5. Test all scripts in new locations\n\nThis reorganization will improve maintainability and make it easier to find relevant scripts.