docs: Add comprehensive development guidance and align documentation

Major Updates:
- Created DEVELOPMENT_GUIDANCE.md - comprehensive status report and strategic direction
  * Full project assessment (75-85% complete)
  * Current status: Phases 2.5-3.1 built (85%), integration needed
  * Development strategy: Continue using Claude Code, defer LLM API integration
  * Priority initiatives: Phase 3.2 Integration, NXOpen docs, Engineering pipeline
  * Foundation for future: Feature documentation pipeline specification

Key Strategic Decisions:
- LLM API integration deferred - use Claude Code for development
- Phase 3.2 Integration is TOP PRIORITY (2-4 weeks)
- NXOpen documentation access - high priority research initiative
- Engineering feature validation pipeline - foundation for production rigor

Documentation Alignment:
- Updated README.md with current status (75-85% complete)
- Added clear links to DEVELOPMENT_GUIDANCE.md for developers
- Updated DEVELOPMENT.md to reflect Phase 3.2 integration focus
- Corrected status indicators across all docs

New Initiatives Documented:
1. NXOpen Documentation Integration
   - Authenticated access to Siemens docs
   - Leverage NXOpen Python stub files for intellisense
   - Enable LLM to reference NXOpen API during code generation

2. Engineering Feature Documentation Pipeline
   - Auto-generate comprehensive docs for FEA features
   - Human review/approval workflow
   - Validation framework for scientific rigor
   - Foundation for production-ready LLM-generated features

3. Validation Pipeline Framework
   - Request parsing → Code gen → Testing → Review → Integration
   - Ensures traceability and engineering rigor
   - NOT for current dev, but foundation for future users

All documentation now consistent and aligned with strategic direction.

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

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

DEVELOPMENT.md

@@ -2,11 +2,13 @@
 
 > Tactical development tracking - What's done, what's next, what needs work
 
-**Last Updated**: 2025-01-16
-**Current Phase**: Phase 2 - LLM Integration
-**Status**: 🟢 Phase 1 Complete | 🟡 Phase 2 Starting
+**Last Updated**: 2025-11-17
+**Current Phase**: Phase 3.2 - Integration Sprint
+**Status**: 🟢 Phase 1 Complete | ✅ Phases 2.5-3.1 Built (85%) | 🎯 Phase 3.2 Integration TOP PRIORITY
 
-For the strategic vision and long-term roadmap, see [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md).
+📘 **Strategic Direction**: See [DEVELOPMENT_GUIDANCE.md](DEVELOPMENT_GUIDANCE.md) for comprehensive status, priorities, and development strategy.
+
+📘 **Long-Term Vision**: See [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md) for the complete roadmap.
 
 ---
 
@@ -23,31 +25,36 @@ For the strategic vision and long-term roadmap, see [DEVELOPMENT_ROADMAP.md](DEV
 
 ## Current Phase
 
-### Phase 2: LLM Integration Layer (🟡 In Progress)
+### Phase 3.2: Integration Sprint (🎯 TOP PRIORITY)
 
-**Goal**: Enable natural language control of Atomizer
+**Goal**: Connect LLM intelligence components to production workflow
 
-**Timeline**: 2 weeks (Started 2025-01-16)
+**Timeline**: 2-4 weeks (Started 2025-11-17)
 
-**Priority Todos**:
+**Status**: LLM components built and tested individually (85% complete). Need to wire them into production runner.
 
-#### Week 1: Feature Registry & Claude Skill
-- [ ] Create `optimization_engine/feature_registry.json`
-  - [ ] Extract all result extractors (stress, displacement, mass)
-  - [ ] Document all NX operations (journal execution, expression updates)
-  - [ ] List all hook points and available plugins
-  - [ ] Add function signatures with parameter descriptions
-- [ ] Draft `.claude/skills/atomizer.md`
-  - [ ] Define skill context (project structure, capabilities)
-  - [ ] Add usage examples for common tasks
-  - [ ] Document coding conventions and patterns
-- [ ] Test LLM navigation
-  - [ ] Can find and read relevant files
-  - [ ] Can understand hook system
-  - [ ] Can locate studies and configurations
+**Critical Path**:
 
-#### Week 2: Natural Language Interface
-- [ ] Implement intent classifier
+#### Week 1-2: Runner Integration
+- [ ] Add `--llm` flag to `run_optimization.py`
+- [ ] Connect `LLMOptimizationRunner` to production workflow
+- [ ] Implement fallback to manual mode if LLM generation fails
+- [ ] End-to-end test: Natural language → NX solve → Results
+- [ ] Performance profiling and optimization
+- [ ] Error handling and graceful degradation
+
+#### Week 3: Documentation & Examples
+- [ ] Update README with LLM capabilities
+- [ ] Create `examples/llm_optimization_example.py`
+- [ ] Write LLM troubleshooting guide
+- [ ] Update all session summaries
+- [ ] Create demo video/GIF
+
+#### Week 4: NXOpen Documentation Research
+- [ ] Investigate Siemens documentation portal access
+- [ ] Test authenticated WebFetch capabilities
+- [ ] Explore NXOpen stub files for intellisense
+- [ ] Document findings and recommendations
   - [ ] "Create study" intent
   - [ ] "Configure optimization" intent
   - [ ] "Analyze results" intent

README.md

@@ -29,7 +29,13 @@ Atomizer enables engineers to:
 - **Extensible Architecture**: Plugin system with hooks for pre/post mesh, solve, and extraction phases
 - **Self-Improving**: Feature registry that learns from user workflows and expands capabilities
 
-📘 See [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md) for the complete vision and implementation plan.
+---
+
+📘 **For Developers**: See [DEVELOPMENT_GUIDANCE.md](DEVELOPMENT_GUIDANCE.md) for comprehensive status report, current priorities, and strategic direction.
+
+📘 **Vision & Roadmap**: See [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md) for the long-term vision and phase-by-phase implementation plan.
+
+📘 **Development Status**: See [DEVELOPMENT.md](DEVELOPMENT.md) for detailed task tracking and completed work.
 
 ## Architecture
 
@@ -164,10 +170,24 @@ python run_5trial_test.py
 - **Web Dashboard**: Real-time monitoring and configuration UI
 - **Example Study**: Bracket displacement maximization with full substudy workflow
 
-**🚀 What's Next**: Natural language optimization configuration via LLM interface (Phase 2)
+## Current Status
 
-For detailed development status and todos, see [DEVELOPMENT.md](DEVELOPMENT.md).
-For the long-term vision, see [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md).
+**Development Phase**: Alpha - 75-85% Complete
+
+- ✅ **Phase 1 (Plugin System)**: 100% Complete & Production Ready
+- ✅ **Phases 2.5-3.1 (LLM Intelligence)**: 85% Complete - Components built and tested
+- 🎯 **Phase 3.2 (Integration)**: **TOP PRIORITY** - Connect LLM features to production workflow
+- 🔬 **Phase 3.4 (NXOpen Docs)**: Research & investigation phase
+
+**What's Working**:
+- Complete optimization engine with Optuna + NX Simcenter
+- Substudy system with live history tracking
+- LLM components (workflow analyzer, code generators, research agent) - tested individually
+- 20-trial optimization validated with real results
+
+**Current Focus**: Integrating LLM components into production runner for end-to-end workflow.
+
+See [DEVELOPMENT_GUIDANCE.md](DEVELOPMENT_GUIDANCE.md) for comprehensive status and priorities.
 
 ## Project Structure