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>

.claude/skills/00_BOOTSTRAP.md

@@ -1,6 +1,16 @@
+---
+skill_id: SKILL_000
+version: 2.0
+last_updated: 2025-12-07
+type: bootstrap
+code_dependencies: []
+requires_skills: []
+---
+
 # Atomizer LLM Bootstrap
 
-**Version**: 1.0
+**Version**: 2.0
+**Updated**: 2025-12-07
 **Purpose**: First file any LLM session reads. Provides instant orientation and task routing.
 
 ---
@@ -61,7 +71,7 @@ User Request
 
 | User Intent | Keywords | Protocol | Skill to Load | Privilege |
 |-------------|----------|----------|---------------|-----------|
-| Create study | "new", "set up", "create", "optimize" | OP_01 | **create-study-wizard.md** | user |
+| Create study | "new", "set up", "create", "optimize" | OP_01 | **core/study-creation-core.md** | user |
 | Run optimization | "start", "run", "execute", "begin" | OP_02 | - | user |
 | Monitor progress | "status", "progress", "trials", "check" | OP_03 | - | user |
 | Analyze results | "results", "best", "compare", "pareto" | OP_04 | - | user |
@@ -107,15 +117,14 @@ See `02_CONTEXT_LOADER.md` for complete loading rules.
 
 **Quick Reference**:
 ```
-CREATE_STUDY     → create-study-wizard.md (PRIMARY)
-                 → Use: from optimization_engine.study_wizard import StudyWizard, create_study
-                 → modules/extractors-catalog.md (if asks about extractors)
+CREATE_STUDY     → core/study-creation-core.md (PRIMARY)
+                 → SYS_12_EXTRACTOR_LIBRARY.md (extractor reference)
                  → modules/zernike-optimization.md (if telescope/mirror)
                  → modules/neural-acceleration.md (if >50 trials)
 
 RUN_OPTIMIZATION → OP_02_RUN_OPTIMIZATION.md
-                 → SYS_10_IMSO.md (if adaptive)
-                 → SYS_13_DASHBOARD_TRACKING.md (if monitoring)
+                 → SYS_15_METHOD_SELECTOR.md (method recommendation)
+                 → SYS_14_NEURAL_ACCELERATION.md (if neural/turbo)
 
 DEBUG           → OP_06_TROUBLESHOOT.md
                 → Relevant SYS_* based on error type

.claude/skills/01_CHEATSHEET.md

@@ -1,6 +1,19 @@
+---
+skill_id: SKILL_001
+version: 2.0
+last_updated: 2025-12-07
+type: reference
+code_dependencies:
+  - optimization_engine/extractors/__init__.py
+  - optimization_engine/method_selector.py
+requires_skills:
+  - SKILL_000
+---
+
 # Atomizer Quick Reference Cheatsheet
 
-**Version**: 1.0
+**Version**: 2.0
+**Updated**: 2025-12-07
 **Purpose**: Rapid lookup for common operations. "I want X → Use Y"
 
 ---

.claude/skills/02_CONTEXT_LOADER.md

@@ -1,6 +1,17 @@
+---
+skill_id: SKILL_002
+version: 2.0
+last_updated: 2025-12-07
+type: loader
+code_dependencies: []
+requires_skills:
+  - SKILL_000
+---
+
 # Atomizer Context Loader
 
-**Version**: 1.0
+**Version**: 2.0
+**Updated**: 2025-12-07
 **Purpose**: Define what documentation to load based on task type. Ensures LLM sessions have exactly the context needed.
 
 ---
@@ -22,26 +33,29 @@
 
 **Always Load**:
 ```
-.claude/skills/core/study-creation-core.md
+.claude/skills/core/study-creation-core.md  (SKILL_CORE_001)
 ```
 
 **Load If**:
 | Condition | Load |
 |-----------|------|
-| User asks about extractors | `modules/extractors-catalog.md` |
+| User asks about extractors | `docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md` |
 | Telescope/mirror/optics mentioned | `modules/zernike-optimization.md` |
-| >50 trials OR "neural" OR "surrogate" | `modules/neural-acceleration.md` |
+| >50 trials OR "neural" OR "surrogate" | `docs/protocols/system/SYS_14_NEURAL_ACCELERATION.md` |
 | Multi-objective (2+ goals) | `docs/protocols/system/SYS_11_MULTI_OBJECTIVE.md` |
+| Method selection needed | `docs/protocols/system/SYS_15_METHOD_SELECTOR.md` |
 
 **Example Context Stack**:
 ```
 # Simple bracket optimization
 core/study-creation-core.md
+SYS_12_EXTRACTOR_LIBRARY.md
 
 # Mirror optimization with neural acceleration
 core/study-creation-core.md
 modules/zernike-optimization.md
-modules/neural-acceleration.md
+SYS_14_NEURAL_ACCELERATION.md
+SYS_15_METHOD_SELECTOR.md
 ```
 
 ---
@@ -254,9 +268,10 @@ Load Stack:
 User: "I need to optimize my M1 mirror's wavefront error with 200 trials"
 
 Load Stack:
-1. core/study-creation-core.md      # Core study creation
-2. modules/zernike-optimization.md  # Zernike-specific patterns
-3. modules/neural-acceleration.md   # Neural acceleration for 200 trials
+1. core/study-creation-core.md         # Core study creation
+2. modules/zernike-optimization.md     # Zernike-specific patterns
+3. SYS_14_NEURAL_ACCELERATION.md       # Neural acceleration for 200 trials
+4. SYS_15_METHOD_SELECTOR.md           # Method recommendation
 ```
 
 ### Example 3: Multi-Objective Structural
@@ -281,8 +296,8 @@ Load Stack:
 User: "I need to extract thermal gradients from my results"
 
 Load Stack:
-1. EXT_01_CREATE_EXTRACTOR.md       # Extractor creation guide
-2. modules/extractors-catalog.md    # Reference existing patterns
+1. EXT_01_CREATE_EXTRACTOR.md          # Extractor creation guide
+2. SYS_12_EXTRACTOR_LIBRARY.md         # Reference existing patterns
 ```
 
 ---

.claude/skills/core/study-creation-core.md

@@ -1,7 +1,20 @@
+---
+skill_id: SKILL_CORE_001
+version: 2.4
+last_updated: 2025-12-07
+type: core
+code_dependencies:
+  - optimization_engine/base_runner.py
+  - optimization_engine/extractors/__init__.py
+  - optimization_engine/templates/registry.json
+requires_skills: []
+replaces: create-study.md
+---
+
 # Study Creation Core Skill
 
-**Last Updated**: December 6, 2025
-**Version**: 2.3 - Added Model Introspection
+**Version**: 2.4
+**Updated**: 2025-12-07
 **Type**: Core Skill
 
 You are helping the user create a complete Atomizer optimization study from a natural language description.