docs: Consolidate documentation and fix protocol numbering (partial)

Phase 2 of restructuring plan:
- Rename SYS_16_STUDY_INSIGHTS -> SYS_17_STUDY_INSIGHTS
- Rename SYS_17_CONTEXT_ENGINEERING -> SYS_18_CONTEXT_ENGINEERING
- Promote Bootstrap V3.0 (Context Engineering) as default
- Archive old Bootstrap V2.0
- Create knowledge_base/playbook.json for ACE framework
- Add OP_08 (Generate Report) to routing tables
- Add SYS_16-18 to protocol tables
- Update docs/protocols/README.md to version 1.1
- Update CLAUDE.md with new protocols
- Create docs/plans/RESTRUCTURING_PLAN.md for continuation

Remaining: Phase 2.8 (Cheatsheet), Phases 3-6

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

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

docs/protocols/README.md

@@ -1,7 +1,7 @@
 # Atomizer Protocol Operating System (POS)
 
-**Version**: 1.0
-**Last Updated**: 2025-12-05
+**Version**: 1.1
+**Last Updated**: 2026-01-06
 
 ---
 
@@ -22,13 +22,19 @@ protocols/
 │   ├── OP_03_MONITOR_PROGRESS.md
 │   ├── OP_04_ANALYZE_RESULTS.md
 │   ├── OP_05_EXPORT_TRAINING_DATA.md
-│   └── OP_06_TROUBLESHOOT.md
+│   ├── OP_06_TROUBLESHOOT.md
+│   ├── OP_07_DISK_OPTIMIZATION.md
+│   └── OP_08_GENERATE_REPORT.md
 ├── system/                      # Layer 3: Core specifications
 │   ├── SYS_10_IMSO.md
 │   ├── SYS_11_MULTI_OBJECTIVE.md
 │   ├── SYS_12_EXTRACTOR_LIBRARY.md
 │   ├── SYS_13_DASHBOARD_TRACKING.md
-│   └── SYS_14_NEURAL_ACCELERATION.md
+│   ├── SYS_14_NEURAL_ACCELERATION.md
+│   ├── SYS_15_METHOD_SELECTOR.md
+│   ├── SYS_16_SELF_AWARE_TURBO.md
+│   ├── SYS_17_STUDY_INSIGHTS.md
+│   └── SYS_18_CONTEXT_ENGINEERING.md
 └── extensions/                  # Layer 4: Extensibility guides
     ├── EXT_01_CREATE_EXTRACTOR.md
     ├── EXT_02_CREATE_HOOK.md
@@ -56,6 +62,8 @@ Day-to-day how-to guides:
 - **OP_04**: Analyze results
 - **OP_05**: Export training data
 - **OP_06**: Troubleshoot issues
+- **OP_07**: Disk optimization (free space)
+- **OP_08**: Generate study report
 
 ### Layer 3: System (`system/`)
 Core technical specifications:
@@ -65,6 +73,9 @@ Core technical specifications:
 - **SYS_13**: Real-Time Dashboard Tracking
 - **SYS_14**: Neural Network Acceleration
 - **SYS_15**: Method Selector
+- **SYS_16**: Self-Aware Turbo (SAT) Method
+- **SYS_17**: Study Insights (Physics Visualization)
+- **SYS_18**: Context Engineering (ACE Framework)
 
 ### Layer 4: Extensions (`extensions/`)
 Guides for extending Atomizer:
@@ -130,6 +141,8 @@ LOAD_WITH: [{dependencies}]
 | Analyze results | [OP_04](operations/OP_04_ANALYZE_RESULTS.md) |
 | Export neural data | [OP_05](operations/OP_05_EXPORT_TRAINING_DATA.md) |
 | Fix errors | [OP_06](operations/OP_06_TROUBLESHOOT.md) |
+| Free disk space | [OP_07](operations/OP_07_DISK_OPTIMIZATION.md) |
+| Generate report | [OP_08](operations/OP_08_GENERATE_REPORT.md) |
 | Add extractor | [EXT_01](extensions/EXT_01_CREATE_EXTRACTOR.md) |
 
 ### By Protocol Number
@@ -142,6 +155,9 @@ LOAD_WITH: [{dependencies}]
 | 13 | Dashboard | [System](system/SYS_13_DASHBOARD_TRACKING.md) |
 | 14 | Neural | [System](system/SYS_14_NEURAL_ACCELERATION.md) |
 | 15 | Method Selector | [System](system/SYS_15_METHOD_SELECTOR.md) |
+| 16 | Self-Aware Turbo | [System](system/SYS_16_SELF_AWARE_TURBO.md) |
+| 17 | Study Insights | [System](system/SYS_17_STUDY_INSIGHTS.md) |
+| 18 | Context Engineering | [System](system/SYS_18_CONTEXT_ENGINEERING.md) |
 
 ---
 
@@ -160,3 +176,4 @@ LOAD_WITH: [{dependencies}]
 | Version | Date | Changes |
 |---------|------|---------|
 | 1.0 | 2025-12-05 | Initial Protocol Operating System |
+| 1.1 | 2026-01-06 | Added OP_07, OP_08; SYS_16, SYS_17, SYS_18; Fixed SYS_16 duplication |