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/command-memory.yml

@@ -49,4 +49,4 @@ Pattern Learning:
   Success Patterns: Learn from effective approaches
   Error Prevention: Remember failure patterns to avoid
   User Preferences: Adapt to individual working styles
-```
+```