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/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
 ```
 
 ---