docs: Final documentation polish and consistency fixes

- Update README.md with LLM assistant section
- Create optimization_memory JSONL structure
- Move implementation plans from skills/modules to docs/plans
- Verify all imports work correctly

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

README.md

@@ -315,6 +315,25 @@ Atomizer/
 
 ---
 
+## For AI Assistants
+
+Atomizer is designed for LLM-first interaction. Key resources:
+
+- **[CLAUDE.md](CLAUDE.md)** - System instructions for Claude Code
+- **[.claude/skills/](/.claude/skills/)** - LLM skill modules
+- **[docs/protocols/](docs/protocols/)** - Protocol Operating System
+
+### Knowledge Base (LAC)
+
+The Learning Atomizer Core (`knowledge_base/lac/`) accumulates optimization knowledge:
+- `session_insights/` - Learnings from past sessions
+- `optimization_memory/` - Optimization outcomes by geometry type
+- `playbook.json` - ACE framework knowledge store
+
+For detailed AI interaction guidance, see CLAUDE.md.
+
+---
+
 ## Environment
 
 **Critical**: Always use the `atomizer` conda environment: