feat: Implement Agentic Architecture for robust session workflows

Phase 1 - Session Bootstrap:
- Add .claude/ATOMIZER_CONTEXT.md as single entry point for new sessions
- Add study state detection and task routing

Phase 2 - Code Deduplication:
- Add optimization_engine/base_runner.py (ConfigDrivenRunner)
- Add optimization_engine/generic_surrogate.py (ConfigDrivenSurrogate)
- Add optimization_engine/study_state.py for study detection
- Add optimization_engine/templates/ with registry and templates
- Studies now require ~50 lines instead of ~300

Phase 3 - Skill Consolidation:
- Add YAML frontmatter metadata to all skills (versioning, dependencies)
- Consolidate create-study.md into core/study-creation-core.md
- Update 00_BOOTSTRAP.md, 01_CHEATSHEET.md, 02_CONTEXT_LOADER.md

Phase 4 - Self-Expanding Knowledge:
- Add optimization_engine/auto_doc.py for auto-generating documentation
- Generate docs/generated/EXTRACTORS.md (27 extractors documented)
- Generate docs/generated/TEMPLATES.md (6 templates)
- Generate docs/generated/EXTRACTOR_CHEATSHEET.md

Phase 5 - Subagent Implementation:
- Add .claude/commands/study-builder.md (create studies)
- Add .claude/commands/nx-expert.md (NX Open API)
- Add .claude/commands/protocol-auditor.md (config validation)
- Add .claude/commands/results-analyzer.md (results analysis)

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

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

docs/generated/TEMPLATES.md

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+# Atomizer Study Templates
+
+*Auto-generated: 2025-12-07 12:53*
+
+Available templates for quick study creation.
+
+---
+
+## Template Reference
+
+| Template | Objectives | Extractors |
+|----------|------------|------------|
+| `Multi-Objective Structural` | mass, stress, stiffness | E1, E3, E4 |
+| `Frequency Optimization` | frequency, mass | E2, E4 |
+| `Mass Minimization` | mass | E1, E3, E4 |
+| `Mirror Wavefront Optimization` | zernike_rms | E8, E9, E10 |
+| `Thermal-Structural Coupled` | max_temperature, thermal_stress | E3, E15, E16 |
+| `Shell Structure Optimization` | mass, stress | E1, E3, E4 |
+
+---
+
+## Multi-Objective Structural
+
+**Description**: NSGA-II optimization for structural analysis with mass, stress, and stiffness objectives
+
+**Category**: structural
+**Solver**: SOL 101
+**Sampler**: NSGAIISampler
+**Turbo Suitable**: Yes
+
+**Example Study**: `bracket_pareto_3obj`
+
+**Objectives**:
+- mass (minimize) - Extractor: E4
+- stress (minimize) - Extractor: E3
+- stiffness (maximize) - Extractor: E1
+
+**Extractors Used**:
+- E1
+- E3
+- E4
+
+**Recommended Trials**:
+- discovery: 1
+- validation: 3
+- quick: 20
+- full: 50
+- comprehensive: 100
+
+---
+
+## Frequency Optimization
+
+**Description**: Maximize natural frequency while minimizing mass for vibration-sensitive structures
+
+**Category**: dynamics
+**Solver**: SOL 103
+**Sampler**: NSGAIISampler
+**Turbo Suitable**: Yes
+
+**Example Study**: `uav_arm_optimization`
+
+**Objectives**:
+- frequency (maximize) - Extractor: E2
+- mass (minimize) - Extractor: E4
+
+**Extractors Used**:
+- E2
+- E4
+
+**Recommended Trials**:
+- discovery: 1
+- validation: 3
+- quick: 20
+- full: 50
+
+---
+
+## Mass Minimization
+
+**Description**: Minimize mass subject to stress and displacement constraints
+
+**Category**: structural
+**Solver**: SOL 101
+**Sampler**: TPESampler
+**Turbo Suitable**: Yes
+
+**Example Study**: `bracket_stiffness_optimization_V3`
+
+**Objectives**:
+- mass (minimize) - Extractor: E4
+
+**Extractors Used**:
+- E1
+- E3
+- E4
+
+**Recommended Trials**:
+- discovery: 1
+- validation: 3
+- quick: 30
+- full: 100
+
+---
+
+## Mirror Wavefront Optimization
+
+**Description**: Minimize Zernike wavefront error for optical mirror deformation
+
+**Category**: optics
+**Solver**: SOL 101
+**Sampler**: TPESampler
+**Turbo Suitable**: No
+
+**Example Study**: `m1_mirror_zernike_optimization`
+
+**Objectives**:
+- zernike_rms (minimize) - Extractor: E8
+
+**Extractors Used**:
+- E8
+- E9
+- E10
+
+**Recommended Trials**:
+- discovery: 1
+- validation: 3
+- quick: 30
+- full: 100
+
+---
+
+## Thermal-Structural Coupled
+
+**Description**: Optimize for thermal and structural performance
+
+**Category**: multiphysics
+**Solver**: SOL 153/400
+**Sampler**: NSGAIISampler
+**Turbo Suitable**: No
+
+**Example Study**: `None`
+
+**Objectives**:
+- max_temperature (minimize) - Extractor: E15
+- thermal_stress (minimize) - Extractor: E3
+
+**Extractors Used**:
+- E3
+- E15
+- E16
+
+**Recommended Trials**:
+- discovery: 1
+- validation: 3
+- quick: 20
+- full: 50
+
+---
+
+## Shell Structure Optimization
+
+**Description**: Optimize shell structures (CQUAD4/CTRIA3) for mass and stress
+
+**Category**: structural
+**Solver**: SOL 101
+**Sampler**: NSGAIISampler
+**Turbo Suitable**: Yes
+
+**Example Study**: `beam_pareto_4var`
+
+**Objectives**:
+- mass (minimize) - Extractor: E4
+- stress (minimize) - Extractor: E3
+
+**Extractors Used**:
+- E1
+- E3
+- E4
+
+**Recommended Trials**:
+- discovery: 1
+- validation: 3
+- quick: 20
+- full: 50
+
+---