Clean up references to deleted scripts and pattern system

- Removed references to validate-references.sh from YAML files
- Removed expand-references.sh from settings.local.json
- Cleaned up @pattern/@flags references from shared files
- Updated documentation to reflect current no-code implementation
- Simplified reference-index.yml to remove @include patterns

This cleanup removes confusion from the abandoned pattern reference
system while maintaining all functionality.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

.claude/commands/shared/cleanup-patterns.yml

@@ -104,4 +104,4 @@ Rollback:
   - Git commit before cleanup
   - Backup configs before changes
   - Document what was removed
-```
+```