refactor: Remove Module 2 Resources content while preserving work

- Removed smart-file-analysis module and all Resources references
- Renumbered modules: GitHub Actions (2), HF Hub (3), Slack (4)
- Updated all cross-references and documentation
- Focused on Tools and Prompts as core MCP primitives

The full Module 2 implementation is preserved at tag: preserve-module2-resources-full

Author: zealoushacker