Enhance skill generator documentation and templates

- Updated Phase 1 and Phase 2 documentation to include next phase links and data flow details.
- Expanded Phase 5 documentation to include comprehensive validation and README generation steps, along with validation report structure.
- Added purpose and usage context sections to various action and script templates (e.g., autonomous-action, llm-action, script-bash).
- Improved commands management by simplifying the command scanning logic and enabling/disabling commands through renaming files.
- Enhanced dashboard command manager to format group names and display nested groups with appropriate icons and colors.
- Updated LiteLLM executor to allow model overrides during execution.
- Added action reference guide and template reference sections to the skill-tuning SKILL.md for better navigation and understanding.

Author: catlog22